├── .gitignore ├── Makefile ├── Makefile.inc ├── copyrights ├── COPYING └── LICENSE.txt ├── src ├── FastQValidator.cpp └── Makefile └── test ├── .gitignore ├── FastQValidatorTest.sh ├── Makefile ├── README.txt ├── expectedResults ├── ExpectedResults0Errors.txt ├── ExpectedResults10Errors.txt ├── ExpectedResults10Errors5Report.txt ├── ExpectedResultsAutoDetect.txt ├── ExpectedResultsAutoDetectBGZ.txt ├── ExpectedResultsAutoDetectBGZnoeof.txt ├── ExpectedResultsAutoDetectBGZnoeofFail.txt ├── ExpectedResultsAutoDetectGZ.txt ├── ExpectedResultsBase.txt ├── ExpectedResultsBaseCompNoMessages.txt ├── ExpectedResultsColor.txt ├── ExpectedResultsColorLimitError.txt ├── ExpectedResultsDisableSeqID.txt ├── ExpectedResultsInterleaved.txt ├── ExpectedResultsMinRead2.txt ├── ExpectedResultsNoBaseComp.txt ├── ExpectedResultsNoBaseCompNoErrors.txt └── ExpectedResultsTestFile2.txt ├── interleaved.fastq ├── testFile.txt.bgz ├── testFile.txt.gz ├── testFile.txt.noeof.bgz └── testFile2.txt /.gitignore: -------------------------------------------------------------------------------- 1 | bin/ 2 | obj/ 3 | *~ 4 | *.tgz 5 | test/testFile.txt -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | SUBDIRS = src 2 | 3 | PARENT_MAKE := Makefile.tool 4 | include Makefile.inc 5 | -------------------------------------------------------------------------------- /Makefile.inc: -------------------------------------------------------------------------------- 1 | # Makefile that includes this should specify PARENT_MAKE to be 2 | # the Makefile it should include from libStatGen/Makefiles/$(PARENT_MAKE) 3 | 4 | # Update version as necessary. 5 | VERSION=0.1.1a 6 | 7 | ######################## 8 | # Library Path: 9 | # 10 | # Default path to the statgen library. You can either update your copy of 11 | # this Makefile to be where you want to get the Makefile from or you can 12 | # overwrite LIB_PATH_GENERAL or LIB_PATH_FASTQ_VALIDATOR. 13 | # This design is such that if you have multiple programs, you could just set 14 | # LIB_PATH_GENERAL to the location they should all use to find the library. 15 | # If one program needs a different path, you would set LIB_PATH_FASTQ_VALIDATOR 16 | # to that different path. 17 | CURRENT_PATH := $(dir $(lastword $(MAKEFILE_LIST))) 18 | LIB_PATH_GENERAL ?=../libStatGen 19 | LIB_PATH_FASTQ_VALIDATOR ?= $(LIB_PATH_GENERAL) 20 | 21 | # add any additional ../ as necessary if it is a relative path 22 | ACTUAL_PATH := $(if $(filter-out /%,$(LIB_PATH_FASTQ_VALIDATOR)), \ 23 | $(addprefix $(CURRENT_PATH), $(LIB_PATH_FASTQ_VALIDATOR)), \ 24 | $(LIB_PATH_FASTQ_VALIDATOR)) 25 | INCLUDE_MAKE = $(ACTUAL_PATH)/Makefiles/$(PARENT_MAKE) 26 | 27 | ######################## 28 | # Include the base Makefile 29 | include $(INCLUDE_MAKE) 30 | 31 | .phony: cloneLib 32 | 33 | ######################## 34 | # This is to handle the case where the statgen library is not already there. 35 | $(INCLUDE_MAKE): 36 | @echo Unable to locate: $(INCLUDE_MAKE) 37 | @echo To change the location, set LIB_PATH_GENERAL or LIB_PATH_FASTQ_VALIDATOR to the appropriate path to libStatGen. Or specify \"make LIB_PATH_GENERAL=yourPath\" or \"make LIB_PATH_FASTQ_VALIDATOR=yourPath\" 38 | @echo Use make cloneLib if you have git and want to clone the current libStatGen at that location. 39 | 40 | 41 | cloneLib: 42 | @if test -d $(LIB_PATH_FASTQ_VALIDATOR); \ 43 | then echo $(LIB_PATH_FASTQ_VALIDATOR) already exists; \ 44 | else git clone git://github.com/statgen/libStatGen.git $(LIB_PATH_FASTQ_VALIDATOR); fi 45 | @echo Call make to compile libStatGen and this tool. 46 | -------------------------------------------------------------------------------- /copyrights/COPYING: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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If the Program does not specify a version number of the 576 | GNU General Public License, you may choose any version ever published 577 | by the Free Software Foundation. 578 | 579 | If the Program specifies that a proxy can decide which future 580 | versions of the GNU General Public License can be used, that proxy's 581 | public statement of acceptance of a version permanently authorizes you 582 | to choose that version for the Program. 583 | 584 | Later license versions may give you additional or different 585 | permissions. However, no additional obligations are imposed on any 586 | author or copyright holder as a result of your choosing to follow a 587 | later version. 588 | 589 | 15. Disclaimer of Warranty. 590 | 591 | THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY 592 | APPLICABLE LAW. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | 676 | -------------------------------------------------------------------------------- /copyrights/LICENSE.txt: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (c) 2009 Regents of the University of Michigan 3 | * 4 | * Permission is hereby granted, free of charge, to any person 5 | * obtaining a copy of this software and associated documentation 6 | * files (the "Software"), to deal in the Software without 7 | * restriction, including without limitation the rights to use, 8 | * copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | * copies of the Software, and to permit persons to whom the 10 | * Software is furnished to do so, subject to the following 11 | * conditions: 12 | * 13 | * The above copyright notice and this permission notice shall be 14 | * included in all copies or substantial portions of the Software. 15 | * 16 | * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 17 | * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES 18 | * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 19 | * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT 20 | * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, 21 | * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING 22 | * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR 23 | * OTHER DEALINGS IN THE SOFTWARE. 24 | */ 25 | 26 | -------------------------------------------------------------------------------- /src/FastQValidator.cpp: -------------------------------------------------------------------------------- 1 | /* 2 | * Copyright (C) 2010-2012 Regents of the University of Michigan 3 | * 4 | * This program is free software: you can redistribute it and/or modify 5 | * it under the terms of the GNU General Public License as published by 6 | * the Free Software Foundation, either version 3 of the License, or 7 | * (at your option) any later version. 8 | * 9 | * This program is distributed in the hope that it will be useful, 10 | * but WITHOUT ANY WARRANTY; without even the implied warranty of 11 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 12 | * GNU General Public License for more details. 13 | * 14 | * You should have received a copy of the GNU General Public License 15 | * along with this program. If not, see . 16 | */ 17 | 18 | #include 19 | 20 | #include "StringArray.h" 21 | #include "StringHash.h" 22 | #include "Parameters.h" 23 | #include "FastQFile.h" 24 | #include "BgzfFileType.h" 25 | 26 | int main(int argc, char ** argv) 27 | { 28 | ParameterList inputParameters; 29 | String filename; 30 | int minReadLength = 10; 31 | int printableErrors = 20; 32 | int maxErrors = -1; 33 | String testParam; 34 | BaseAsciiMap::SPACE_TYPE myBaseType = BaseAsciiMap::UNKNOWN; 35 | 36 | // Read the parameters from the command line. 37 | bool baseSpace = false; 38 | bool colorSpace = false; 39 | bool autoDetect = false; 40 | bool ignoreErrors = false; 41 | bool baseComposition = false; 42 | bool avgQual = false; 43 | bool quiet = false; 44 | bool noeof = false; 45 | bool params = false; 46 | bool disableSeqIDCheck = false; 47 | bool interleaved = false; 48 | 49 | BEGIN_LONG_PARAMETERS(longParameterList) 50 | LONG_STRINGPARAMETER("file", &filename) 51 | LONG_PARAMETER("baseComposition", &baseComposition) 52 | LONG_PARAMETER("avgQual", &avgQual) 53 | LONG_PARAMETER("disableSeqIDCheck", &disableSeqIDCheck) 54 | LONG_PARAMETER("interleaved", &interleaved) 55 | LONG_PARAMETER("noeof", &noeof) 56 | LONG_PARAMETER("quiet", &quiet) 57 | LONG_PARAMETER("params", ¶ms) 58 | LONG_INTPARAMETER("minReadLen", &minReadLength) 59 | LONG_INTPARAMETER("maxErrors", &maxErrors) 60 | LONG_PARAMETER_GROUP("Space Type") 61 | EXCLUSIVE_PARAMETER("baseSpace", &baseSpace) 62 | EXCLUSIVE_PARAMETER("colorSpace", &colorSpace) 63 | EXCLUSIVE_PARAMETER("auto", &autoDetect) 64 | LONG_PARAMETER_GROUP("Errors") 65 | EXCLUSIVE_PARAMETER("ignoreErrors", &ignoreErrors) 66 | LONG_SMARTINTPARAMETER("printableErrors", &printableErrors) 67 | BEGIN_LEGACY_PARAMETERS() 68 | LONG_PARAMETER("printBaseComp", &baseComposition) 69 | LONG_PARAMETER("disableAllMessages", &quiet) 70 | LONG_INTPARAMETER("quitAfterErrorNum", &maxErrors) 71 | LONG_PARAMETER_GROUP("Space Type") 72 | EXCLUSIVE_PARAMETER("baseSpace", &baseSpace) 73 | EXCLUSIVE_PARAMETER("colorSpace", &colorSpace) 74 | EXCLUSIVE_PARAMETER("autoDetect", &autoDetect) 75 | LONG_PARAMETER_GROUP("Errors") 76 | EXCLUSIVE_PARAMETER("ignoreAllErrors", &ignoreErrors) 77 | LONG_SMARTINTPARAMETER("maxReportedErrors", &printableErrors) 78 | END_LONG_PARAMETERS(); 79 | 80 | inputParameters.Add(new LongParameters ("Input Parameters", longParameterList)); 81 | 82 | inputParameters.Read(argc, argv); 83 | 84 | if(ignoreErrors) 85 | { 86 | // Ignore all errors, so set printableErrors to 0. 87 | printableErrors = 0; 88 | } 89 | 90 | // Set the base type based on the passed in parameters. 91 | if(baseSpace) 92 | { 93 | // Base Space 94 | myBaseType = BaseAsciiMap::BASE_SPACE; 95 | } 96 | else if(colorSpace) 97 | { 98 | myBaseType = BaseAsciiMap::COLOR_SPACE; 99 | } 100 | else 101 | { 102 | myBaseType = BaseAsciiMap::UNKNOWN; 103 | // Set autoDetect 104 | autoDetect = true; 105 | } 106 | 107 | // If no eof block is required for a bgzf file, set the bgzf file type to 108 | // not look for it. 109 | if(noeof) 110 | { 111 | // Set that the eof block is not required. 112 | BgzfFileType::setRequireEofBlock(false); 113 | } 114 | 115 | // DO not print status if set to quiet. 116 | if((!quiet) && params) 117 | { 118 | inputParameters.Status(); 119 | } 120 | 121 | if(filename == "") 122 | { 123 | if(quiet) 124 | { 125 | return(-1); 126 | } 127 | // No filename was specified so print a usage description. 128 | std::cout << "ERROR: No filename specified. See below for usage help."; 129 | std::cout << std::endl << std::endl; 130 | 131 | std::cout << " Required Parameters:" << std::endl; 132 | std::cout << "\t--file : FastQ filename with path to be prorcessed.\n"; 133 | std::cout << std::endl; 134 | 135 | std::cout << " Optional Parameters:" << std::endl; 136 | std::cout << "\t--minReadLen : Minimum allowed read length (Defaults to 10).\n"; 137 | std::cout << "\t--maxErrors : Number of errors to allow before quitting\n"; 138 | std::cout << "\t reading/validating the file.\n"; 139 | std::cout << "\t -1 (default) indicates to not quit until\n"; 140 | std::cout << "\t the entire file is read.\n"; 141 | std::cout << "\t 0 indicates not to read/validate anything\n"; 142 | std::cout << "\t--printableErrors : Maximum number of errors to print before\n"; 143 | std::cout << "\t suppressing them (Defaults to 20).\n"; 144 | std::cout << "\t Different than maxErrors since \n"; 145 | std::cout << "\t printableErrors will continue reading and\n"; 146 | std::cout << "\t validating the file until the end, but\n"; 147 | std::cout << "\t just doesn't print the errors.\n"; 148 | std::cout << "\t--ignoreErrors : Ignore all errors (same as printableErrors = 0)\n"; 149 | std::cout << "\t overwrites the printableErrors option.\n"; 150 | std::cout << "\t--baseComposition : Print the Base Composition Statistics.\n"; 151 | std::cout << "\t--avgQual : Print the average phred quality per cycle & overall average quality.\n"; 152 | std::cout << "\t--disableSeqIDCheck : Disable the unique sequence identifier check.\n"; 153 | std::cout << "\t Use this option to save memory since the sequence id\n"; 154 | std::cout << "\t check uses a lot of memory.\n"; 155 | std::cout << "\t--noeof : Disable checking that the eof block is present in gzipped files\n."; 156 | std::cout << "\t--interleaved : Validate consequtive reads have the same sequence identifier\n"; 157 | std::cout << "\t (only allowed difference is 1/2, but not required) and validate\n"; 158 | std::cout << "\t that otherwise reads have unique sequence identifiers.\n"; 159 | std::cout << "\t Cannot be used if '--disableSeqIDCheck' is specified.\n"; 160 | std::cout << "\t--params : Print the parameter settings.\n"; 161 | std::cout << "\t--quiet : Suppresses the display of errors and summary statistics.\n"; 162 | std::cout << "\t Does not affect the printing of Base Composition Statistics.\n"; 163 | 164 | std::cout << "\n Optional Space Options for Raw Sequence (Last one specified is used):\n"; 165 | std::cout << "\t--auto : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default).\n"; 166 | std::cout << "\t--baseSpace : ACTGN only\n"; 167 | std::cout << "\t--colorSpace : 0123. only\n"; 168 | std::cout << std::endl; 169 | 170 | std::cout << " Usage:" << std::endl; 171 | std::cout << "\t./fastQValidator --file [--minReadLen ] [--maxErrors ] [--printableErrors |--ignoreErrors] [--baseComposition] [--disableSeqIDCheck] [--interleaved] [--quiet] [--baseSpace|--colorSpace|--auto] [--params]\n\n"; 172 | std::cout << " Examples:" << std::endl; 173 | std::cout << "\t../fastQValidator --file testFile.txt\n"; 174 | std::cout << "\t../fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100\n"; 175 | std::cout << "\t./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreErrors\n"; 176 | std::cout << std::endl; 177 | return (-1); 178 | } 179 | 180 | FastQFile validator(minReadLength, printableErrors); 181 | 182 | if(quiet) 183 | { 184 | validator.disableMessages(); 185 | } 186 | 187 | if(disableSeqIDCheck) 188 | { 189 | validator.disableSeqIDCheck(); 190 | } 191 | 192 | if(interleaved) 193 | { 194 | validator.interleaved(); 195 | } 196 | 197 | if(interleaved && disableSeqIDCheck) 198 | { 199 | if(!quiet) 200 | { 201 | std::cout << "ERROR: --interleaved and --disableSeqIDCheck cannot both be specified.\n"; 202 | } 203 | return(-1); 204 | } 205 | 206 | validator.setMaxErrors(maxErrors); 207 | 208 | FastQStatus::Status status = validator.validateFastQFile(filename, baseComposition, myBaseType, avgQual); 209 | 210 | if(!quiet) 211 | { 212 | std::cout << "Returning: " << status << " : " << FastQStatus::getStatusString(status) 213 | << std::endl; 214 | } 215 | 216 | return(status); 217 | } 218 | -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- 1 | # Name of the executable 2 | EXE=fastQValidator 3 | ######################## 4 | # The Files: 5 | TOOLBASE = 6 | SRCONLY = FastQValidator.cpp 7 | HDRONLY = 8 | 9 | ######################## 10 | # Include the base Makefile 11 | PARENT_MAKE = Makefile.src 12 | include ../Makefile.inc 13 | -------------------------------------------------------------------------------- /test/.gitignore: -------------------------------------------------------------------------------- 1 | results/ -------------------------------------------------------------------------------- /test/FastQValidatorTest.sh: -------------------------------------------------------------------------------- 1 | PATH_TO_EXE="../bin" 2 | 3 | ERROR=false 4 | 5 | # Test running on a non-fastq file 6 | $PATH_TO_EXE/fastQValidator --params --file ../src/FastQValidator.cpp > results/nonFastQFileResults.txt 2>&1 7 | 8 | 9 | # Run on test file that tests all types of errors detected by the 10 | # FastQValidator. Specify to autodetect space type from the file 11 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --auto --printableErrors 100 --baseComposition > results/runResults.txt 2>&1 12 | diff results/runResults.txt expectedResults/ExpectedResultsAutoDetect.txt 13 | if [ $? -ne 0 ] 14 | then 15 | ERROR=true 16 | fi 17 | 18 | # Run on gz file 19 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt.gz --minReadLen 10 --auto --printableErrors 100 --baseComposition > results/runResultsGZ.txt 2>&1 20 | diff results/runResultsGZ.txt expectedResults/ExpectedResultsAutoDetectGZ.txt 21 | if [ $? -ne 0 ] 22 | then 23 | ERROR=true 24 | fi 25 | 26 | # Run on bgzf file 27 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt.bgz --minReadLen 10 --auto --printableErrors 100 --baseComposition > results/runResultsBGZ.txt 2>&1 28 | diff results/runResultsBGZ.txt expectedResults/ExpectedResultsAutoDetectBGZ.txt 29 | if [ $? -ne 0 ] 30 | then 31 | ERROR=true 32 | fi 33 | 34 | # Run on bgzf file with no eof causing failure 35 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt.noeof.bgz --minReadLen 10 --auto --printableErrors 100 --baseComposition > results/runResultsBGZnoeofFail.txt 2>&1 36 | diff results/runResultsBGZnoeofFail.txt expectedResults/ExpectedResultsAutoDetectBGZnoeofFail.txt 37 | if [ $? -ne 0 ] 38 | then 39 | ERROR=true 40 | fi 41 | 42 | # Run on bgzf file with no eof but skipping the eof check 43 | $PATH_TO_EXE/fastQValidator --noeof --params --file testFile.txt.noeof.bgz --minReadLen 10 --auto --printableErrors 100 --baseComposition > results/runResultsBGZnoeof.txt 2>&1 44 | diff results/runResultsBGZnoeof.txt expectedResults/ExpectedResultsAutoDetectBGZnoeof.txt 45 | if [ $? -ne 0 ] 46 | then 47 | ERROR=true 48 | fi 49 | 50 | # Run on the same file but do not check for unique sequence id. 51 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --auto --printableErrors 100 --baseComposition --disableSeqIDCheck > results/runResultsDisableSeqID.txt 2>&1 52 | diff results/runResultsDisableSeqID.txt expectedResults/ExpectedResultsDisableSeqID.txt 53 | if [ $? -ne 0 ] 54 | then 55 | ERROR=true 56 | fi 57 | 58 | # Run on the same test file, but specify Base Sequences. 59 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 --baseComposition > results/runResultsBase.txt 2>&1 60 | diff results/runResultsBase.txt expectedResults/ExpectedResultsBase.txt 61 | if [ $? -ne 0 ] 62 | then 63 | ERROR=true 64 | fi 65 | 66 | # Run on the same test file, but specify quit after -1 errors (do not quit until all read). 67 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 --baseComposition --maxErrors -1 > results/runResultsBaseNoQuit.txt 2>&1 68 | diff results/runResultsBaseNoQuit.txt expectedResults/ExpectedResultsBase.txt 69 | if [ $? -ne 0 ] 70 | then 71 | ERROR=true 72 | fi 73 | 74 | # Run on the same test file, but specify quit after 0 errors (do not read the file). 75 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 --baseComposition --maxErrors 0 > results/runResultsBaseQuit0.txt 2>&1 76 | diff results/runResultsBaseQuit0.txt expectedResults/ExpectedResults0Errors.txt 77 | if [ $? -ne 0 ] 78 | then 79 | ERROR=true 80 | fi 81 | 82 | # Run on the same test file, but specify quit after 10 errors, with only reporting the first 5 errors. 83 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 5 --baseComposition --maxErrors 10 > results/runResultsBaseQuit10Err5.txt 2>&1 84 | diff results/runResultsBaseQuit10Err5.txt expectedResults/ExpectedResults10Errors5Report.txt 85 | if [ $? -ne 0 ] 86 | then 87 | ERROR=true 88 | fi 89 | 90 | # Run on the same test file, but specify quit after 10 errors, reporting the first 100 errors, but only 10 will be reported because then it quit. 91 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 --baseComposition --maxErrors 10 > results/runResultsBaseQuit10.txt 2>&1 92 | diff results/runResultsBaseQuit10.txt expectedResults/ExpectedResults10Errors.txt 93 | if [ $? -ne 0 ] 94 | then 95 | ERROR=true 96 | fi 97 | 98 | # Run on the same test file, but specify Base Sequences, do not print baseComp. 99 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 > results/runResultsNoBaseComp.txt 2>&1 100 | diff results/runResultsNoBaseComp.txt expectedResults/ExpectedResultsNoBaseComp.txt 101 | if [ $? -ne 0 ] 102 | then 103 | ERROR=true 104 | fi 105 | 106 | # Run on the same test file, but ignore all errors, do not print baseComp. 107 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --ignoreErrors --avgQual > results/runResultsNoBaseCompNoErrors.txt 2>&1 108 | diff results/runResultsNoBaseCompNoErrors.txt expectedResults/ExpectedResultsNoBaseCompNoErrors.txt 109 | if [ $? -ne 0 ] 110 | then 111 | ERROR=true 112 | fi 113 | 114 | # Run on the same test file, but do not print any messages, print baseComp. 115 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --baseSpace --quiet --baseComposition --avgQual > results/runResultsBaseCompNoMessages.txt 2>&1 116 | diff results/runResultsBaseCompNoMessages.txt expectedResults/ExpectedResultsBaseCompNoMessages.txt 117 | if [ $? -ne 0 ] 118 | then 119 | ERROR=true 120 | fi 121 | 122 | # Run on the same test file, but auto detect as default. 123 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --printableErrors 100 --baseComposition > results/runResultsBaseDefault.txt 2>&1 124 | diff results/runResultsBaseDefault.txt expectedResults/ExpectedResultsAutoDetect.txt 125 | if [ $? -ne 0 ] 126 | then 127 | ERROR=true 128 | fi 129 | 130 | # Run on the same test file, but only accept Color Space Sequences 131 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --colorSpace --printableErrors 300 --baseComposition > results/runResultsColor.txt 2>&1 132 | diff results/runResultsColor.txt expectedResults/ExpectedResultsColor.txt 133 | if [ $? -ne 0 ] 134 | then 135 | ERROR=true 136 | fi 137 | 138 | # Run on the same test file, but only accept Color Space Sequences limit 139 | # number of printed errors to 5. 140 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 10 --colorSpace --printableErrors 5 --baseComposition > results/runResultsColorLimitError.txt 2>&1 141 | diff results/runResultsColorLimitError.txt expectedResults/ExpectedResultsColorLimitError.txt 142 | if [ $? -ne 0 ] 143 | then 144 | ERROR=true 145 | fi 146 | 147 | # Run on test file that tests all types of errors detected by the 148 | # FastQValidator. Accept Base Space as default. 149 | # Modify to set minimum read length to 2. 150 | $PATH_TO_EXE/fastQValidator --params --file testFile.txt --minReadLen 2 --printableErrors 100 --baseComposition > results/runResultsMinRead2.txt 2>&1 151 | diff results/runResultsMinRead2.txt expectedResults/ExpectedResultsMinRead2.txt 152 | if [ $? -ne 0 ] 153 | then 154 | ERROR=true 155 | fi 156 | 157 | # Test on interleaved file 158 | $PATH_TO_EXE/fastQValidator --file interleaved.fastq --interleaved > results/runResultsInterleaved.txt 2>&1 159 | diff results/runResultsInterleaved.txt expectedResults/ExpectedResultsInterleaved.txt 160 | if [ $? -ne 0 ] 161 | then 162 | ERROR=true 163 | fi 164 | 165 | # Test extra empty lines at the end of the file 166 | $PATH_TO_EXE/fastQValidator --file testFile2.txt > results/runResultsTestFile2.txt 2>&1 167 | if [ $? -ne 0 ] 168 | then 169 | ERROR=true 170 | fi 171 | diff results/runResultsTestFile2.txt expectedResults/ExpectedResultsTestFile2.txt 172 | if [ $? -ne 0 ] 173 | then 174 | ERROR=true 175 | fi 176 | 177 | if($ERROR == true) 178 | then 179 | exit 1 180 | fi 181 | 182 | -------------------------------------------------------------------------------- /test/Makefile: -------------------------------------------------------------------------------- 1 | # The command to run. 2 | TEST_COMMAND = ln -sfT $(ACTUAL_PATH)/fastq/test/testFile.txt testFile.txt; \ 3 | mkdir -p results; ./FastQValidatorTest.sh 4 | 5 | TEST_CLEAN = rm -f testFile.txt; rm -rf results; 6 | 7 | ######################## 8 | # Include the base Makefile 9 | PARENT_MAKE = Makefile.test 10 | include ../Makefile.inc 11 | -------------------------------------------------------------------------------- /test/README.txt: -------------------------------------------------------------------------------- 1 | Lines 1 - 24 - test that all valid quality string characters are accepted & tests multiple line Raw Sequence and Quality Strings. 2 | 3 | Sequence Identifier Line Validates: 4 | * Line 25: line is at least 2 characters long ('@' and at least 1 for the sequence identifier) 5 | * Line 29: line starts with an '@' 6 | * Line 33 & 37: no space between the '@' & the sequence identifier (which must be at least 1 character) 7 | * Line 41: sequence identifier is unique within the file 8 | 9 | Raw Sequence Line Validates: 10 | * Line 46 & 47: every character is in ACTGNactgn0123. 11 | * Line 51: the raw sequence after it is completely read is at least a configurable minimum length 12 | * Line 56 & 57: assumes all lines are part of the raw sequence until a line begins with a '+' or the end of the file is reached 13 | 14 | Plus Line Validates: 15 | * Line 88: sequence identifier on + line does not match the one on the @ line. 16 | * Line 91: that this line exists for each sequence 17 | 18 | Quality Line Validates: 19 | * Line 63 & 64: each character is > ascii 32 20 | * Line 70: assumes all lines are part of the quality string until the total length of quality characters is >= the raw sequence length or the end of the file is reached 21 | * Line 77: length of the quality string equals the length of the raw sequence 22 | 23 | 24 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResults0Errors.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors 6 | Space Type : --baseSpace [ON], --colorSpace, --auto 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | 10 | Base Composition Statistics: 11 | Read Index %A %C %G %T %N Total Reads At Index 12 | 13 | Finished processing testFile.txt with 0 lines containing 0 sequences. 14 | There were a total of 0 errors. 15 | ERROR: No FastQSequences in the file. 16 | Returning: 6 : FASTQ_NO_SEQUENCE_ERROR 17 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResults10Errors.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [10] 6 | Space Type : --baseSpace [ON], --colorSpace, --auto 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | 20 | Base Composition Statistics: 21 | Read Index %A %C %G %T %N Total Reads At Index 22 | 0 100.00 0.00 0.00 0.00 0.00 3 23 | 1 0.00 100.00 0.00 0.00 0.00 2 24 | 2 0.00 0.00 0.00 100.00 0.00 2 25 | 3 0.00 0.00 100.00 0.00 0.00 2 26 | 4 50.00 0.00 0.00 0.00 50.00 2 27 | 5 50.00 50.00 0.00 0.00 0.00 2 28 | 6 0.00 50.00 0.00 50.00 0.00 2 29 | 7 0.00 0.00 0.00 50.00 50.00 2 30 | 8 50.00 0.00 0.00 0.00 50.00 2 31 | 9 0.00 50.00 50.00 0.00 0.00 2 32 | 10 0.00 0.00 0.00 100.00 0.00 1 33 | 11 0.00 0.00 0.00 0.00 100.00 1 34 | 12 0.00 0.00 100.00 0.00 0.00 1 35 | 13 100.00 0.00 0.00 0.00 0.00 1 36 | 14 100.00 0.00 0.00 0.00 0.00 1 37 | 15 0.00 100.00 0.00 0.00 0.00 1 38 | 39 | Finished processing testFile.txt with 11 lines containing 3 sequences. 40 | There were a total of 10 errors. 41 | Returning: 1 : FASTQ_INVALID 42 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResults10Errors5Report.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [10] 6 | Space Type : --baseSpace [ON], --colorSpace, --auto 7 | Errors : --ignoreErrors, --printableErrors [5] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | 15 | Base Composition Statistics: 16 | Read Index %A %C %G %T %N Total Reads At Index 17 | 0 100.00 0.00 0.00 0.00 0.00 3 18 | 1 0.00 100.00 0.00 0.00 0.00 2 19 | 2 0.00 0.00 0.00 100.00 0.00 2 20 | 3 0.00 0.00 100.00 0.00 0.00 2 21 | 4 50.00 0.00 0.00 0.00 50.00 2 22 | 5 50.00 50.00 0.00 0.00 0.00 2 23 | 6 0.00 50.00 0.00 50.00 0.00 2 24 | 7 0.00 0.00 0.00 50.00 50.00 2 25 | 8 50.00 0.00 0.00 0.00 50.00 2 26 | 9 0.00 50.00 50.00 0.00 0.00 2 27 | 10 0.00 0.00 0.00 100.00 0.00 1 28 | 11 0.00 0.00 0.00 0.00 100.00 1 29 | 12 0.00 0.00 100.00 0.00 0.00 1 30 | 13 100.00 0.00 0.00 0.00 0.00 1 31 | 14 100.00 0.00 0.00 0.00 0.00 1 32 | 15 0.00 100.00 0.00 0.00 0.00 1 33 | 34 | Finished processing testFile.txt with 11 lines containing 3 sequences. 35 | There were a total of 10 errors. 36 | Returning: 1 : FASTQ_INVALID 37 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsAutoDetect.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 36 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 38 | ERROR on Line 63: Invalid character (' ') in quality string. 39 | ERROR on Line 64: Invalid character (' ') in quality string. 40 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 41 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 42 | ERROR on Line 91: Invalid character ('0') in base sequence. 43 | ERROR on Line 91: Invalid character ('1') in base sequence. 44 | ERROR on Line 91: Invalid character ('2') in base sequence. 45 | ERROR on Line 91: Invalid character ('3') in base sequence. 46 | ERROR on Line 91: Invalid character ('.') in base sequence. 47 | ERROR on Line 91: Invalid character ('0') in base sequence. 48 | ERROR on Line 91: Invalid character ('3') in base sequence. 49 | ERROR on Line 91: Invalid character ('2') in base sequence. 50 | ERROR on Line 91: Invalid character ('1') in base sequence. 51 | ERROR on Line 91: Invalid character ('.') in base sequence. 52 | ERROR on Line 91: Invalid character ('0') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 91: Invalid character ('1') in base sequence. 55 | ERROR on Line 95: Reached the end of the file without a '+' line. 56 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 57 | 58 | Base Composition Statistics: 59 | Read Index %A %C %G %T %N Total Reads At Index 60 | 0 100.00 0.00 0.00 0.00 0.00 20 61 | 1 5.26 94.74 0.00 0.00 0.00 19 62 | 2 5.26 0.00 0.00 94.74 0.00 19 63 | 3 0.00 0.00 94.44 0.00 5.56 18 64 | 4 50.00 38.89 0.00 0.00 11.11 18 65 | 5 52.94 47.06 0.00 0.00 0.00 17 66 | 6 0.00 50.00 0.00 50.00 0.00 18 67 | 7 0.00 0.00 38.89 11.11 50.00 18 68 | 8 44.44 0.00 5.56 0.00 50.00 18 69 | 9 0.00 88.24 11.76 0.00 0.00 17 70 | 10 11.11 0.00 0.00 88.89 0.00 9 71 | 11 0.00 0.00 0.00 0.00 100.00 8 72 | 12 0.00 0.00 100.00 0.00 0.00 8 73 | 13 100.00 0.00 0.00 0.00 0.00 4 74 | 14 33.33 66.67 0.00 0.00 0.00 3 75 | 15 0.00 33.33 0.00 66.67 0.00 3 76 | 16 0.00 0.00 100.00 0.00 0.00 2 77 | 17 100.00 0.00 0.00 0.00 0.00 2 78 | 18 0.00 100.00 0.00 0.00 0.00 2 79 | 19 0.00 0.00 0.00 100.00 0.00 2 80 | 20 0.00 0.00 0.00 0.00 100.00 2 81 | 21 100.00 0.00 0.00 0.00 0.00 2 82 | 22 0.00 100.00 0.00 0.00 0.00 2 83 | 23 0.00 0.00 0.00 100.00 0.00 2 84 | 24 0.00 0.00 0.00 0.00 100.00 2 85 | 25 0.00 0.00 100.00 0.00 0.00 2 86 | 87 | Finished processing testFile.txt with 95 lines containing 21 sequences. 88 | There were a total of 48 errors. 89 | Returning: 1 : FASTQ_INVALID 90 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsAutoDetectBGZ.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt.bgz], --baseComposition [ON], --avgQual, 4 | --disableSeqIDCheck, --interleaved, --noeof, --quiet, 5 | --params [ON], --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 36 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 38 | ERROR on Line 63: Invalid character (' ') in quality string. 39 | ERROR on Line 64: Invalid character (' ') in quality string. 40 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 41 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 42 | ERROR on Line 91: Invalid character ('0') in base sequence. 43 | ERROR on Line 91: Invalid character ('1') in base sequence. 44 | ERROR on Line 91: Invalid character ('2') in base sequence. 45 | ERROR on Line 91: Invalid character ('3') in base sequence. 46 | ERROR on Line 91: Invalid character ('.') in base sequence. 47 | ERROR on Line 91: Invalid character ('0') in base sequence. 48 | ERROR on Line 91: Invalid character ('3') in base sequence. 49 | ERROR on Line 91: Invalid character ('2') in base sequence. 50 | ERROR on Line 91: Invalid character ('1') in base sequence. 51 | ERROR on Line 91: Invalid character ('.') in base sequence. 52 | ERROR on Line 91: Invalid character ('0') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 91: Invalid character ('1') in base sequence. 55 | ERROR on Line 95: Reached the end of the file without a '+' line. 56 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 57 | 58 | Base Composition Statistics: 59 | Read Index %A %C %G %T %N Total Reads At Index 60 | 0 100.00 0.00 0.00 0.00 0.00 20 61 | 1 5.26 94.74 0.00 0.00 0.00 19 62 | 2 5.26 0.00 0.00 94.74 0.00 19 63 | 3 0.00 0.00 94.44 0.00 5.56 18 64 | 4 50.00 38.89 0.00 0.00 11.11 18 65 | 5 52.94 47.06 0.00 0.00 0.00 17 66 | 6 0.00 50.00 0.00 50.00 0.00 18 67 | 7 0.00 0.00 38.89 11.11 50.00 18 68 | 8 44.44 0.00 5.56 0.00 50.00 18 69 | 9 0.00 88.24 11.76 0.00 0.00 17 70 | 10 11.11 0.00 0.00 88.89 0.00 9 71 | 11 0.00 0.00 0.00 0.00 100.00 8 72 | 12 0.00 0.00 100.00 0.00 0.00 8 73 | 13 100.00 0.00 0.00 0.00 0.00 4 74 | 14 33.33 66.67 0.00 0.00 0.00 3 75 | 15 0.00 33.33 0.00 66.67 0.00 3 76 | 16 0.00 0.00 100.00 0.00 0.00 2 77 | 17 100.00 0.00 0.00 0.00 0.00 2 78 | 18 0.00 100.00 0.00 0.00 0.00 2 79 | 19 0.00 0.00 0.00 100.00 0.00 2 80 | 20 0.00 0.00 0.00 0.00 100.00 2 81 | 21 100.00 0.00 0.00 0.00 0.00 2 82 | 22 0.00 100.00 0.00 0.00 0.00 2 83 | 23 0.00 0.00 0.00 100.00 0.00 2 84 | 24 0.00 0.00 0.00 0.00 100.00 2 85 | 25 0.00 0.00 100.00 0.00 0.00 2 86 | 87 | Finished processing testFile.txt.bgz with 95 lines containing 21 sequences. 88 | There were a total of 48 errors. 89 | Returning: 1 : FASTQ_INVALID 90 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsAutoDetectBGZnoeof.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt.noeof.bgz], --baseComposition [ON], --avgQual, 4 | --disableSeqIDCheck, --interleaved, --noeof [ON], --quiet, 5 | --params [ON], --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 36 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 38 | ERROR on Line 63: Invalid character (' ') in quality string. 39 | ERROR on Line 64: Invalid character (' ') in quality string. 40 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 41 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 42 | ERROR on Line 91: Invalid character ('0') in base sequence. 43 | ERROR on Line 91: Invalid character ('1') in base sequence. 44 | ERROR on Line 91: Invalid character ('2') in base sequence. 45 | ERROR on Line 91: Invalid character ('3') in base sequence. 46 | ERROR on Line 91: Invalid character ('.') in base sequence. 47 | ERROR on Line 91: Invalid character ('0') in base sequence. 48 | ERROR on Line 91: Invalid character ('3') in base sequence. 49 | ERROR on Line 91: Invalid character ('2') in base sequence. 50 | ERROR on Line 91: Invalid character ('1') in base sequence. 51 | ERROR on Line 91: Invalid character ('.') in base sequence. 52 | ERROR on Line 91: Invalid character ('0') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 91: Invalid character ('1') in base sequence. 55 | ERROR on Line 95: Reached the end of the file without a '+' line. 56 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 57 | 58 | Base Composition Statistics: 59 | Read Index %A %C %G %T %N Total Reads At Index 60 | 0 100.00 0.00 0.00 0.00 0.00 20 61 | 1 5.26 94.74 0.00 0.00 0.00 19 62 | 2 5.26 0.00 0.00 94.74 0.00 19 63 | 3 0.00 0.00 94.44 0.00 5.56 18 64 | 4 50.00 38.89 0.00 0.00 11.11 18 65 | 5 52.94 47.06 0.00 0.00 0.00 17 66 | 6 0.00 50.00 0.00 50.00 0.00 18 67 | 7 0.00 0.00 38.89 11.11 50.00 18 68 | 8 44.44 0.00 5.56 0.00 50.00 18 69 | 9 0.00 88.24 11.76 0.00 0.00 17 70 | 10 11.11 0.00 0.00 88.89 0.00 9 71 | 11 0.00 0.00 0.00 0.00 100.00 8 72 | 12 0.00 0.00 100.00 0.00 0.00 8 73 | 13 100.00 0.00 0.00 0.00 0.00 4 74 | 14 33.33 66.67 0.00 0.00 0.00 3 75 | 15 0.00 33.33 0.00 66.67 0.00 3 76 | 16 0.00 0.00 100.00 0.00 0.00 2 77 | 17 100.00 0.00 0.00 0.00 0.00 2 78 | 18 0.00 100.00 0.00 0.00 0.00 2 79 | 19 0.00 0.00 0.00 100.00 0.00 2 80 | 20 0.00 0.00 0.00 0.00 100.00 2 81 | 21 100.00 0.00 0.00 0.00 0.00 2 82 | 22 0.00 100.00 0.00 0.00 0.00 2 83 | 23 0.00 0.00 0.00 100.00 0.00 2 84 | 24 0.00 0.00 0.00 0.00 100.00 2 85 | 25 0.00 0.00 100.00 0.00 0.00 2 86 | 87 | Finished processing testFile.txt.noeof.bgz with 95 lines containing 21 sequences. 88 | There were a total of 48 errors. 89 | Returning: 1 : FASTQ_INVALID 90 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsAutoDetectBGZnoeofFail.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt.noeof.bgz], --baseComposition [ON], --avgQual, 4 | --disableSeqIDCheck, --interleaved, --noeof, --quiet, 5 | --params [ON], --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | BGZF EOF marker is missing in testFile.txt.noeof.bgz 10 | ERROR: Failed to open file: testFile.txt.noeof.bgz 11 | Returning: 3 : FASTQ_OPEN_ERROR 12 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsAutoDetectGZ.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt.gz], --baseComposition [ON], --avgQual, 4 | --disableSeqIDCheck, --interleaved, --noeof, --quiet, 5 | --params [ON], --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 36 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 38 | ERROR on Line 63: Invalid character (' ') in quality string. 39 | ERROR on Line 64: Invalid character (' ') in quality string. 40 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 41 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 42 | ERROR on Line 91: Invalid character ('0') in base sequence. 43 | ERROR on Line 91: Invalid character ('1') in base sequence. 44 | ERROR on Line 91: Invalid character ('2') in base sequence. 45 | ERROR on Line 91: Invalid character ('3') in base sequence. 46 | ERROR on Line 91: Invalid character ('.') in base sequence. 47 | ERROR on Line 91: Invalid character ('0') in base sequence. 48 | ERROR on Line 91: Invalid character ('3') in base sequence. 49 | ERROR on Line 91: Invalid character ('2') in base sequence. 50 | ERROR on Line 91: Invalid character ('1') in base sequence. 51 | ERROR on Line 91: Invalid character ('.') in base sequence. 52 | ERROR on Line 91: Invalid character ('0') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 91: Invalid character ('1') in base sequence. 55 | ERROR on Line 95: Reached the end of the file without a '+' line. 56 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 57 | 58 | Base Composition Statistics: 59 | Read Index %A %C %G %T %N Total Reads At Index 60 | 0 100.00 0.00 0.00 0.00 0.00 20 61 | 1 5.26 94.74 0.00 0.00 0.00 19 62 | 2 5.26 0.00 0.00 94.74 0.00 19 63 | 3 0.00 0.00 94.44 0.00 5.56 18 64 | 4 50.00 38.89 0.00 0.00 11.11 18 65 | 5 52.94 47.06 0.00 0.00 0.00 17 66 | 6 0.00 50.00 0.00 50.00 0.00 18 67 | 7 0.00 0.00 38.89 11.11 50.00 18 68 | 8 44.44 0.00 5.56 0.00 50.00 18 69 | 9 0.00 88.24 11.76 0.00 0.00 17 70 | 10 11.11 0.00 0.00 88.89 0.00 9 71 | 11 0.00 0.00 0.00 0.00 100.00 8 72 | 12 0.00 0.00 100.00 0.00 0.00 8 73 | 13 100.00 0.00 0.00 0.00 0.00 4 74 | 14 33.33 66.67 0.00 0.00 0.00 3 75 | 15 0.00 33.33 0.00 66.67 0.00 3 76 | 16 0.00 0.00 100.00 0.00 0.00 2 77 | 17 100.00 0.00 0.00 0.00 0.00 2 78 | 18 0.00 100.00 0.00 0.00 0.00 2 79 | 19 0.00 0.00 0.00 100.00 0.00 2 80 | 20 0.00 0.00 0.00 0.00 100.00 2 81 | 21 100.00 0.00 0.00 0.00 0.00 2 82 | 22 0.00 100.00 0.00 0.00 0.00 2 83 | 23 0.00 0.00 0.00 100.00 0.00 2 84 | 24 0.00 0.00 0.00 0.00 100.00 2 85 | 25 0.00 0.00 100.00 0.00 0.00 2 86 | 87 | Finished processing testFile.txt.gz with 95 lines containing 21 sequences. 88 | There were a total of 48 errors. 89 | Returning: 1 : FASTQ_INVALID 90 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsBase.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace [ON], --colorSpace, --auto 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 36 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 38 | ERROR on Line 63: Invalid character (' ') in quality string. 39 | ERROR on Line 64: Invalid character (' ') in quality string. 40 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 41 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 42 | ERROR on Line 91: Invalid character ('0') in base sequence. 43 | ERROR on Line 91: Invalid character ('1') in base sequence. 44 | ERROR on Line 91: Invalid character ('2') in base sequence. 45 | ERROR on Line 91: Invalid character ('3') in base sequence. 46 | ERROR on Line 91: Invalid character ('.') in base sequence. 47 | ERROR on Line 91: Invalid character ('0') in base sequence. 48 | ERROR on Line 91: Invalid character ('3') in base sequence. 49 | ERROR on Line 91: Invalid character ('2') in base sequence. 50 | ERROR on Line 91: Invalid character ('1') in base sequence. 51 | ERROR on Line 91: Invalid character ('.') in base sequence. 52 | ERROR on Line 91: Invalid character ('0') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 91: Invalid character ('1') in base sequence. 55 | ERROR on Line 95: Reached the end of the file without a '+' line. 56 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 57 | 58 | Base Composition Statistics: 59 | Read Index %A %C %G %T %N Total Reads At Index 60 | 0 100.00 0.00 0.00 0.00 0.00 20 61 | 1 5.26 94.74 0.00 0.00 0.00 19 62 | 2 5.26 0.00 0.00 94.74 0.00 19 63 | 3 0.00 0.00 94.44 0.00 5.56 18 64 | 4 50.00 38.89 0.00 0.00 11.11 18 65 | 5 52.94 47.06 0.00 0.00 0.00 17 66 | 6 0.00 50.00 0.00 50.00 0.00 18 67 | 7 0.00 0.00 38.89 11.11 50.00 18 68 | 8 44.44 0.00 5.56 0.00 50.00 18 69 | 9 0.00 88.24 11.76 0.00 0.00 17 70 | 10 11.11 0.00 0.00 88.89 0.00 9 71 | 11 0.00 0.00 0.00 0.00 100.00 8 72 | 12 0.00 0.00 100.00 0.00 0.00 8 73 | 13 100.00 0.00 0.00 0.00 0.00 4 74 | 14 33.33 66.67 0.00 0.00 0.00 3 75 | 15 0.00 33.33 0.00 66.67 0.00 3 76 | 16 0.00 0.00 100.00 0.00 0.00 2 77 | 17 100.00 0.00 0.00 0.00 0.00 2 78 | 18 0.00 100.00 0.00 0.00 0.00 2 79 | 19 0.00 0.00 0.00 100.00 0.00 2 80 | 20 0.00 0.00 0.00 0.00 100.00 2 81 | 21 100.00 0.00 0.00 0.00 0.00 2 82 | 22 0.00 100.00 0.00 0.00 0.00 2 83 | 23 0.00 0.00 0.00 100.00 0.00 2 84 | 24 0.00 0.00 0.00 0.00 100.00 2 85 | 25 0.00 0.00 100.00 0.00 0.00 2 86 | 87 | Finished processing testFile.txt with 95 lines containing 21 sequences. 88 | There were a total of 48 errors. 89 | Returning: 1 : FASTQ_INVALID 90 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsBaseCompNoMessages.txt: -------------------------------------------------------------------------------- 1 | 2 | Base Composition Statistics: 3 | Read Index %A %C %G %T %N Total Reads At Index 4 | 0 100.00 0.00 0.00 0.00 0.00 20 5 | 1 5.26 94.74 0.00 0.00 0.00 19 6 | 2 5.26 0.00 0.00 94.74 0.00 19 7 | 3 0.00 0.00 94.44 0.00 5.56 18 8 | 4 50.00 38.89 0.00 0.00 11.11 18 9 | 5 52.94 47.06 0.00 0.00 0.00 17 10 | 6 0.00 50.00 0.00 50.00 0.00 18 11 | 7 0.00 0.00 38.89 11.11 50.00 18 12 | 8 44.44 0.00 5.56 0.00 50.00 18 13 | 9 0.00 88.24 11.76 0.00 0.00 17 14 | 10 11.11 0.00 0.00 88.89 0.00 9 15 | 11 0.00 0.00 0.00 0.00 100.00 8 16 | 12 0.00 0.00 100.00 0.00 0.00 8 17 | 13 100.00 0.00 0.00 0.00 0.00 4 18 | 14 33.33 66.67 0.00 0.00 0.00 3 19 | 15 0.00 33.33 0.00 66.67 0.00 3 20 | 16 0.00 0.00 100.00 0.00 0.00 2 21 | 17 100.00 0.00 0.00 0.00 0.00 2 22 | 18 0.00 100.00 0.00 0.00 0.00 2 23 | 19 0.00 0.00 0.00 100.00 0.00 2 24 | 20 0.00 0.00 0.00 0.00 100.00 2 25 | 21 100.00 0.00 0.00 0.00 0.00 2 26 | 22 0.00 100.00 0.00 0.00 0.00 2 27 | 23 0.00 0.00 0.00 100.00 0.00 2 28 | 24 0.00 0.00 0.00 0.00 100.00 2 29 | 25 0.00 0.00 100.00 0.00 0.00 2 30 | 31 | 32 | Average Phred Quality by Read Index (starts at 0): 33 | Read Index Average Quality 34 | 0 44.10 35 | 1 45.55 36 | 2 51.11 37 | 3 47.68 38 | 4 47.37 39 | 5 43.63 40 | 6 48.37 41 | 7 48.47 42 | 8 53.28 43 | 9 50.00 44 | 10 52.62 45 | 11 49.69 46 | 12 51.08 47 | 13 47.20 48 | 14 45.75 49 | 15 57.67 50 | 16 72.00 51 | 17 73.00 52 | 18 74.00 53 | 19 75.00 54 | 20 47.50 55 | 21 77.00 56 | 22 78.00 57 | 23 79.00 58 | 24 80.00 59 | 25 80.50 60 | 61 | Overall Average Phred Quality = 50.40 62 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsColor.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace [ON], --auto 7 | Errors : --ignoreErrors, --printableErrors [300] 8 | 9 | ERROR on Line 2: Invalid character ('C') in base sequence. 10 | ERROR on Line 2: Invalid character ('T') in base sequence. 11 | ERROR on Line 2: Invalid character ('G') in base sequence. 12 | ERROR on Line 2: Invalid character ('N') in base sequence. 13 | ERROR on Line 2: Invalid character ('a') in base sequence. 14 | ERROR on Line 2: Invalid character ('c') in base sequence. 15 | ERROR on Line 2: Invalid character ('t') in base sequence. 16 | ERROR on Line 2: Invalid character ('n') in base sequence. 17 | ERROR on Line 2: Invalid character ('g') in base sequence. 18 | ERROR on Line 6: Invalid character ('C') in base sequence. 19 | ERROR on Line 6: Invalid character ('T') in base sequence. 20 | ERROR on Line 6: Invalid character ('G') in base sequence. 21 | ERROR on Line 6: Invalid character ('A') in base sequence. 22 | ERROR on Line 6: Invalid character ('C') in base sequence. 23 | ERROR on Line 6: Invalid character ('T') in base sequence. 24 | ERROR on Line 6: Invalid character ('N') in base sequence. 25 | ERROR on Line 6: Invalid character ('a') in base sequence. 26 | ERROR on Line 6: Invalid character ('c') in base sequence. 27 | ERROR on Line 6: Invalid character ('t') in base sequence. 28 | ERROR on Line 6: Invalid character ('n') in base sequence. 29 | ERROR on Line 6: Invalid character ('g') in base sequence. 30 | ERROR on Line 6: Invalid character ('a') in base sequence. 31 | ERROR on Line 6: Invalid character ('a') in base sequence. 32 | ERROR on Line 6: Invalid character ('c') in base sequence. 33 | ERROR on Line 15: Invalid character ('C') in base sequence. 34 | ERROR on Line 15: Invalid character ('T') in base sequence. 35 | ERROR on Line 15: Invalid character ('G') in base sequence. 36 | ERROR on Line 15: Invalid character ('A') in base sequence. 37 | ERROR on Line 15: Invalid character ('C') in base sequence. 38 | ERROR on Line 15: Invalid character ('T') in base sequence. 39 | ERROR on Line 15: Invalid character ('N') in base sequence. 40 | ERROR on Line 16: Invalid character ('a') in base sequence. 41 | ERROR on Line 16: Invalid character ('c') in base sequence. 42 | ERROR on Line 16: Invalid character ('t') in base sequence. 43 | ERROR on Line 16: Invalid character ('n') in base sequence. 44 | ERROR on Line 16: Invalid character ('g') in base sequence. 45 | ERROR on Line 16: Invalid character ('A') in base sequence. 46 | ERROR on Line 16: Invalid character ('C') in base sequence. 47 | ERROR on Line 16: Invalid character ('T') in base sequence. 48 | ERROR on Line 16: Invalid character ('G') in base sequence. 49 | ERROR on Line 16: Invalid character ('A') in base sequence. 50 | ERROR on Line 16: Invalid character ('C') in base sequence. 51 | ERROR on Line 16: Invalid character ('T') in base sequence. 52 | ERROR on Line 16: Invalid character ('N') in base sequence. 53 | ERROR on Line 16: Invalid character ('a') in base sequence. 54 | ERROR on Line 16: Invalid character ('c') in base sequence. 55 | ERROR on Line 16: Invalid character ('t') in base sequence. 56 | ERROR on Line 16: Invalid character ('n') in base sequence. 57 | ERROR on Line 16: Invalid character ('g') in base sequence. 58 | ERROR on Line 21: Invalid character ('C') in base sequence. 59 | ERROR on Line 21: Invalid character ('T') in base sequence. 60 | ERROR on Line 21: Invalid character ('G') in base sequence. 61 | ERROR on Line 21: Invalid character ('A') in base sequence. 62 | ERROR on Line 21: Invalid character ('C') in base sequence. 63 | ERROR on Line 21: Invalid character ('T') in base sequence. 64 | ERROR on Line 21: Invalid character ('N') in base sequence. 65 | ERROR on Line 21: Invalid character ('a') in base sequence. 66 | ERROR on Line 21: Invalid character ('c') in base sequence. 67 | ERROR on Line 21: Invalid character ('t') in base sequence. 68 | ERROR on Line 21: Invalid character ('n') in base sequence. 69 | ERROR on Line 21: Invalid character ('g') in base sequence. 70 | ERROR on Line 22: Invalid character ('A') in base sequence. 71 | ERROR on Line 22: Invalid character ('C') in base sequence. 72 | ERROR on Line 22: Invalid character ('T') in base sequence. 73 | ERROR on Line 22: Invalid character ('G') in base sequence. 74 | ERROR on Line 22: Invalid character ('A') in base sequence. 75 | ERROR on Line 22: Invalid character ('C') in base sequence. 76 | ERROR on Line 22: Invalid character ('T') in base sequence. 77 | ERROR on Line 22: Invalid character ('N') in base sequence. 78 | ERROR on Line 22: Invalid character ('a') in base sequence. 79 | ERROR on Line 22: Invalid character ('c') in base sequence. 80 | ERROR on Line 22: Invalid character ('t') in base sequence. 81 | ERROR on Line 22: Invalid character ('n') in base sequence. 82 | ERROR on Line 22: Invalid character ('g') in base sequence. 83 | ERROR on Line 25: The sequence identifier line was too short. 84 | ERROR on Line 26: Invalid character ('C') in base sequence. 85 | ERROR on Line 26: Invalid character ('T') in base sequence. 86 | ERROR on Line 26: Invalid character ('G') in base sequence. 87 | ERROR on Line 26: Invalid character ('A') in base sequence. 88 | ERROR on Line 26: Invalid character ('C') in base sequence. 89 | ERROR on Line 26: Invalid character ('T') in base sequence. 90 | ERROR on Line 26: Invalid character ('N') in base sequence. 91 | ERROR on Line 26: Invalid character ('a') in base sequence. 92 | ERROR on Line 26: Invalid character ('c') in base sequence. 93 | ERROR on Line 26: Invalid character ('t') in base sequence. 94 | ERROR on Line 26: Invalid character ('n') in base sequence. 95 | ERROR on Line 26: Invalid character ('g') in base sequence. 96 | ERROR on Line 29: First line of a sequence does not begin with @ 97 | ERROR on Line 30: Invalid character ('C') in base sequence. 98 | ERROR on Line 30: Invalid character ('T') in base sequence. 99 | ERROR on Line 30: Invalid character ('G') in base sequence. 100 | ERROR on Line 30: Invalid character ('A') in base sequence. 101 | ERROR on Line 30: Invalid character ('C') in base sequence. 102 | ERROR on Line 30: Invalid character ('T') in base sequence. 103 | ERROR on Line 30: Invalid character ('N') in base sequence. 104 | ERROR on Line 30: Invalid character ('a') in base sequence. 105 | ERROR on Line 30: Invalid character ('c') in base sequence. 106 | ERROR on Line 30: Invalid character ('t') in base sequence. 107 | ERROR on Line 30: Invalid character ('n') in base sequence. 108 | ERROR on Line 30: Invalid character ('g') in base sequence. 109 | ERROR on Line 33: No Sequence Identifier specified before the comment. 110 | ERROR on Line 34: Invalid character ('C') in base sequence. 111 | ERROR on Line 34: Invalid character ('T') in base sequence. 112 | ERROR on Line 34: Invalid character ('G') in base sequence. 113 | ERROR on Line 34: Invalid character ('A') in base sequence. 114 | ERROR on Line 34: Invalid character ('C') in base sequence. 115 | ERROR on Line 34: Invalid character ('T') in base sequence. 116 | ERROR on Line 34: Invalid character ('N') in base sequence. 117 | ERROR on Line 34: Invalid character ('a') in base sequence. 118 | ERROR on Line 34: Invalid character ('c') in base sequence. 119 | ERROR on Line 34: Invalid character ('t') in base sequence. 120 | ERROR on Line 34: Invalid character ('n') in base sequence. 121 | ERROR on Line 34: Invalid character ('g') in base sequence. 122 | ERROR on Line 37: No Sequence Identifier specified before the comment. 123 | ERROR on Line 38: Invalid character ('C') in base sequence. 124 | ERROR on Line 38: Invalid character ('T') in base sequence. 125 | ERROR on Line 38: Invalid character ('G') in base sequence. 126 | ERROR on Line 38: Invalid character ('A') in base sequence. 127 | ERROR on Line 38: Invalid character ('C') in base sequence. 128 | ERROR on Line 38: Invalid character ('T') in base sequence. 129 | ERROR on Line 38: Invalid character ('N') in base sequence. 130 | ERROR on Line 38: Invalid character ('a') in base sequence. 131 | ERROR on Line 38: Invalid character ('c') in base sequence. 132 | ERROR on Line 38: Invalid character ('t') in base sequence. 133 | ERROR on Line 38: Invalid character ('n') in base sequence. 134 | ERROR on Line 38: Invalid character ('g') in base sequence. 135 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 136 | ERROR on Line 42: Invalid character ('C') in base sequence. 137 | ERROR on Line 42: Invalid character ('T') in base sequence. 138 | ERROR on Line 42: Invalid character ('G') in base sequence. 139 | ERROR on Line 42: Invalid character ('N') in base sequence. 140 | ERROR on Line 42: Invalid character ('a') in base sequence. 141 | ERROR on Line 42: Invalid character ('c') in base sequence. 142 | ERROR on Line 42: Invalid character ('t') in base sequence. 143 | ERROR on Line 42: Invalid character ('n') in base sequence. 144 | ERROR on Line 42: Invalid character ('g') in base sequence. 145 | ERROR on Line 46: Invalid character ('C') in base sequence. 146 | ERROR on Line 46: Invalid character ('T') in base sequence. 147 | ERROR on Line 46: Invalid character ('N') in base sequence. 148 | ERROR on Line 46: Invalid character ('a') in base sequence. 149 | ERROR on Line 46: Invalid character ('H') in base sequence. 150 | ERROR on Line 46: Invalid character ('t') in base sequence. 151 | ERROR on Line 46: Invalid character ('n') in base sequence. 152 | ERROR on Line 46: Invalid character ('g') in base sequence. 153 | ERROR on Line 47: Invalid character ('a') in base sequence. 154 | ERROR on Line 47: Invalid character ('B') in base sequence. 155 | ERROR on Line 47: Invalid character ('Z') in base sequence. 156 | ERROR on Line 47: Invalid character ('a') in base sequence. 157 | ERROR on Line 51: Invalid character ('a') in base sequence. 158 | ERROR on Line 51: Invalid character ('a') in base sequence. 159 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 160 | ERROR on Line 55: Invalid character ('C') in base sequence. 161 | ERROR on Line 55: Invalid character ('T') in base sequence. 162 | ERROR on Line 55: Invalid character ('G') in base sequence. 163 | ERROR on Line 55: Invalid character ('A') in base sequence. 164 | ERROR on Line 55: Invalid character ('C') in base sequence. 165 | ERROR on Line 55: Invalid character ('T') in base sequence. 166 | ERROR on Line 55: Invalid character ('N') in base sequence. 167 | ERROR on Line 55: Invalid character ('a') in base sequence. 168 | ERROR on Line 55: Invalid character ('c') in base sequence. 169 | ERROR on Line 55: Invalid character ('t') in base sequence. 170 | ERROR on Line 55: Invalid character ('n') in base sequence. 171 | ERROR on Line 55: Invalid character ('g') in base sequence. 172 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 173 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 174 | ERROR on Line 61: Invalid character ('C') in base sequence. 175 | ERROR on Line 61: Invalid character ('T') in base sequence. 176 | ERROR on Line 61: Invalid character ('G') in base sequence. 177 | ERROR on Line 61: Invalid character ('C') in base sequence. 178 | ERROR on Line 61: Invalid character ('a') in base sequence. 179 | ERROR on Line 61: Invalid character ('c') in base sequence. 180 | ERROR on Line 61: Invalid character ('g') in base sequence. 181 | ERROR on Line 61: Invalid character ('n') in base sequence. 182 | ERROR on Line 61: Invalid character ('c') in base sequence. 183 | ERROR on Line 63: Invalid character (' ') in quality string. 184 | ERROR on Line 64: Invalid character (' ') in quality string. 185 | ERROR on Line 66: Invalid character ('C') in base sequence. 186 | ERROR on Line 66: Invalid character ('T') in base sequence. 187 | ERROR on Line 66: Invalid character ('G') in base sequence. 188 | ERROR on Line 66: Invalid character ('C') in base sequence. 189 | ERROR on Line 67: Invalid character ('a') in base sequence. 190 | ERROR on Line 67: Invalid character ('c') in base sequence. 191 | ERROR on Line 67: Invalid character ('g') in base sequence. 192 | ERROR on Line 67: Invalid character ('n') in base sequence. 193 | ERROR on Line 67: Invalid character ('c') in base sequence. 194 | ERROR on Line 73: Invalid character ('C') in base sequence. 195 | ERROR on Line 73: Invalid character ('T') in base sequence. 196 | ERROR on Line 73: Invalid character ('G') in base sequence. 197 | ERROR on Line 73: Invalid character ('C') in base sequence. 198 | ERROR on Line 74: Invalid character ('a') in base sequence. 199 | ERROR on Line 74: Invalid character ('c') in base sequence. 200 | ERROR on Line 74: Invalid character ('g') in base sequence. 201 | ERROR on Line 74: Invalid character ('n') in base sequence. 202 | ERROR on Line 74: Invalid character ('c') in base sequence. 203 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 204 | ERROR on Line 79: Invalid character ('C') in base sequence. 205 | ERROR on Line 79: Invalid character ('T') in base sequence. 206 | ERROR on Line 79: Invalid character ('G') in base sequence. 207 | ERROR on Line 79: Invalid character ('C') in base sequence. 208 | ERROR on Line 79: Invalid character ('a') in base sequence. 209 | ERROR on Line 79: Invalid character ('c') in base sequence. 210 | ERROR on Line 79: Invalid character ('g') in base sequence. 211 | ERROR on Line 79: Invalid character ('n') in base sequence. 212 | ERROR on Line 79: Invalid character ('c') in base sequence. 213 | ERROR on Line 83: Invalid character ('C') in base sequence. 214 | ERROR on Line 83: Invalid character ('T') in base sequence. 215 | ERROR on Line 83: Invalid character ('G') in base sequence. 216 | ERROR on Line 83: Invalid character ('C') in base sequence. 217 | ERROR on Line 83: Invalid character ('a') in base sequence. 218 | ERROR on Line 83: Invalid character ('c') in base sequence. 219 | ERROR on Line 83: Invalid character ('g') in base sequence. 220 | ERROR on Line 83: Invalid character ('n') in base sequence. 221 | ERROR on Line 83: Invalid character ('c') in base sequence. 222 | ERROR on Line 87: Invalid character ('C') in base sequence. 223 | ERROR on Line 87: Invalid character ('T') in base sequence. 224 | ERROR on Line 87: Invalid character ('G') in base sequence. 225 | ERROR on Line 87: Invalid character ('C') in base sequence. 226 | ERROR on Line 87: Invalid character ('a') in base sequence. 227 | ERROR on Line 87: Invalid character ('c') in base sequence. 228 | ERROR on Line 87: Invalid character ('g') in base sequence. 229 | ERROR on Line 87: Invalid character ('n') in base sequence. 230 | ERROR on Line 87: Invalid character ('c') in base sequence. 231 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 232 | ERROR on Line 91: Invalid character ('0') in base sequence. 233 | ERROR on Line 95: Invalid character ('C') in base sequence. 234 | ERROR on Line 95: Invalid character ('T') in base sequence. 235 | ERROR on Line 95: Invalid character ('G') in base sequence. 236 | ERROR on Line 95: Invalid character ('C') in base sequence. 237 | ERROR on Line 95: Invalid character ('a') in base sequence. 238 | ERROR on Line 95: Invalid character ('c') in base sequence. 239 | ERROR on Line 95: Invalid character ('g') in base sequence. 240 | ERROR on Line 95: Invalid character ('n') in base sequence. 241 | ERROR on Line 95: Invalid character ('c') in base sequence. 242 | ERROR on Line 95: Reached the end of the file without a '+' line. 243 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 244 | 245 | Base Composition Statistics: 246 | Read Index %A %C %G %T %N Total Reads At Index 247 | 0 100.00 0.00 0.00 0.00 0.00 20 248 | 1 0.00 100.00 0.00 0.00 0.00 2 249 | 2 0.00 0.00 100.00 0.00 0.00 2 250 | 3 0.00 0.00 0.00 100.00 0.00 2 251 | 4 0.00 0.00 0.00 0.00 100.00 2 252 | 5 100.00 0.00 0.00 0.00 0.00 2 253 | 6 0.00 0.00 0.00 100.00 0.00 2 254 | 7 0.00 0.00 100.00 0.00 0.00 2 255 | 8 0.00 100.00 0.00 0.00 0.00 2 256 | 9 33.33 0.00 0.00 0.00 66.67 3 257 | 10 66.67 0.00 0.00 0.00 33.33 3 258 | 11 33.33 66.67 0.00 0.00 0.00 3 259 | 12 0.00 100.00 0.00 0.00 0.00 3 260 | 13 0.00 0.00 100.00 0.00 0.00 1 261 | 14 0.00 0.00 0.00 100.00 0.00 1 262 | 15 No Valid Bases found. 263 | 16 No Valid Bases found. 264 | 17 No Valid Bases found. 265 | 18 No Valid Bases found. 266 | 19 No Valid Bases found. 267 | 20 No Valid Bases found. 268 | 21 No Valid Bases found. 269 | 22 No Valid Bases found. 270 | 23 No Valid Bases found. 271 | 24 No Valid Bases found. 272 | 25 No Valid Bases found. 273 | 274 | Finished processing testFile.txt with 95 lines containing 21 sequences. 275 | There were a total of 235 errors. 276 | Returning: 1 : FASTQ_INVALID 277 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsColorLimitError.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace [ON], --auto 7 | Errors : --ignoreErrors, --printableErrors [5] 8 | 9 | ERROR on Line 2: Invalid character ('C') in base sequence. 10 | ERROR on Line 2: Invalid character ('T') in base sequence. 11 | ERROR on Line 2: Invalid character ('G') in base sequence. 12 | ERROR on Line 2: Invalid character ('N') in base sequence. 13 | ERROR on Line 2: Invalid character ('a') in base sequence. 14 | 15 | Base Composition Statistics: 16 | Read Index %A %C %G %T %N Total Reads At Index 17 | 0 100.00 0.00 0.00 0.00 0.00 20 18 | 1 0.00 100.00 0.00 0.00 0.00 2 19 | 2 0.00 0.00 100.00 0.00 0.00 2 20 | 3 0.00 0.00 0.00 100.00 0.00 2 21 | 4 0.00 0.00 0.00 0.00 100.00 2 22 | 5 100.00 0.00 0.00 0.00 0.00 2 23 | 6 0.00 0.00 0.00 100.00 0.00 2 24 | 7 0.00 0.00 100.00 0.00 0.00 2 25 | 8 0.00 100.00 0.00 0.00 0.00 2 26 | 9 33.33 0.00 0.00 0.00 66.67 3 27 | 10 66.67 0.00 0.00 0.00 33.33 3 28 | 11 33.33 66.67 0.00 0.00 0.00 3 29 | 12 0.00 100.00 0.00 0.00 0.00 3 30 | 13 0.00 0.00 100.00 0.00 0.00 1 31 | 14 0.00 0.00 0.00 100.00 0.00 1 32 | 15 No Valid Bases found. 33 | 16 No Valid Bases found. 34 | 17 No Valid Bases found. 35 | 18 No Valid Bases found. 36 | 19 No Valid Bases found. 37 | 20 No Valid Bases found. 38 | 21 No Valid Bases found. 39 | 22 No Valid Bases found. 40 | 23 No Valid Bases found. 41 | 24 No Valid Bases found. 42 | 25 No Valid Bases found. 43 | 44 | Finished processing testFile.txt with 95 lines containing 21 sequences. 45 | There were a total of 235 errors. 46 | Returning: 1 : FASTQ_INVALID 47 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsDisableSeqID.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, 4 | --disableSeqIDCheck [ON], --interleaved, --noeof, --quiet, 5 | --params [ON], --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 46: Invalid character ('H') in base sequence. 31 | ERROR on Line 46: Invalid character ('0') in base sequence. 32 | ERROR on Line 47: Invalid character ('B') in base sequence. 33 | ERROR on Line 47: Invalid character ('Z') in base sequence. 34 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 35 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 36 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 63: Invalid character (' ') in quality string. 38 | ERROR on Line 64: Invalid character (' ') in quality string. 39 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 40 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 41 | ERROR on Line 91: Invalid character ('0') in base sequence. 42 | ERROR on Line 91: Invalid character ('1') in base sequence. 43 | ERROR on Line 91: Invalid character ('2') in base sequence. 44 | ERROR on Line 91: Invalid character ('3') in base sequence. 45 | ERROR on Line 91: Invalid character ('.') in base sequence. 46 | ERROR on Line 91: Invalid character ('0') in base sequence. 47 | ERROR on Line 91: Invalid character ('3') in base sequence. 48 | ERROR on Line 91: Invalid character ('2') in base sequence. 49 | ERROR on Line 91: Invalid character ('1') in base sequence. 50 | ERROR on Line 91: Invalid character ('.') in base sequence. 51 | ERROR on Line 91: Invalid character ('0') in base sequence. 52 | ERROR on Line 91: Invalid character ('1') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 95: Reached the end of the file without a '+' line. 55 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 56 | 57 | Base Composition Statistics: 58 | Read Index %A %C %G %T %N Total Reads At Index 59 | 0 100.00 0.00 0.00 0.00 0.00 20 60 | 1 5.26 94.74 0.00 0.00 0.00 19 61 | 2 5.26 0.00 0.00 94.74 0.00 19 62 | 3 0.00 0.00 94.44 0.00 5.56 18 63 | 4 50.00 38.89 0.00 0.00 11.11 18 64 | 5 52.94 47.06 0.00 0.00 0.00 17 65 | 6 0.00 50.00 0.00 50.00 0.00 18 66 | 7 0.00 0.00 38.89 11.11 50.00 18 67 | 8 44.44 0.00 5.56 0.00 50.00 18 68 | 9 0.00 88.24 11.76 0.00 0.00 17 69 | 10 11.11 0.00 0.00 88.89 0.00 9 70 | 11 0.00 0.00 0.00 0.00 100.00 8 71 | 12 0.00 0.00 100.00 0.00 0.00 8 72 | 13 100.00 0.00 0.00 0.00 0.00 4 73 | 14 33.33 66.67 0.00 0.00 0.00 3 74 | 15 0.00 33.33 0.00 66.67 0.00 3 75 | 16 0.00 0.00 100.00 0.00 0.00 2 76 | 17 100.00 0.00 0.00 0.00 0.00 2 77 | 18 0.00 100.00 0.00 0.00 0.00 2 78 | 19 0.00 0.00 0.00 100.00 0.00 2 79 | 20 0.00 0.00 0.00 0.00 100.00 2 80 | 21 100.00 0.00 0.00 0.00 0.00 2 81 | 22 0.00 100.00 0.00 0.00 0.00 2 82 | 23 0.00 0.00 0.00 100.00 0.00 2 83 | 24 0.00 0.00 0.00 0.00 100.00 2 84 | 25 0.00 0.00 100.00 0.00 0.00 2 85 | 86 | Finished processing testFile.txt with 95 lines containing 21 sequences. 87 | There were a total of 47 errors. 88 | Returning: 1 : FASTQ_INVALID 89 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsInterleaved.txt: -------------------------------------------------------------------------------- 1 | ERROR on Line 21: Interleaved: consecutive reads do not have matching sequence identifiers: 3/3 and 3/1 2 | ERROR on Line 37: Interleaved: consecutive reads do not have matching sequence identifiers: 5 and 5/1 3 | Finished processing interleaved.fastq with 56 lines containing 14 sequences. 4 | There were a total of 2 errors. 5 | Returning: 1 : FASTQ_INVALID 6 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsMinRead2.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition [ON], --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [2], --maxErrors [-1] 6 | Space Type : --baseSpace, --colorSpace, --auto [ON] 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 36 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 63: Invalid character (' ') in quality string. 38 | ERROR on Line 64: Invalid character (' ') in quality string. 39 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 40 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 41 | ERROR on Line 91: Invalid character ('0') in base sequence. 42 | ERROR on Line 91: Invalid character ('1') in base sequence. 43 | ERROR on Line 91: Invalid character ('2') in base sequence. 44 | ERROR on Line 91: Invalid character ('3') in base sequence. 45 | ERROR on Line 91: Invalid character ('.') in base sequence. 46 | ERROR on Line 91: Invalid character ('0') in base sequence. 47 | ERROR on Line 91: Invalid character ('3') in base sequence. 48 | ERROR on Line 91: Invalid character ('2') in base sequence. 49 | ERROR on Line 91: Invalid character ('1') in base sequence. 50 | ERROR on Line 91: Invalid character ('.') in base sequence. 51 | ERROR on Line 91: Invalid character ('0') in base sequence. 52 | ERROR on Line 91: Invalid character ('1') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 95: Reached the end of the file without a '+' line. 55 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 56 | 57 | Base Composition Statistics: 58 | Read Index %A %C %G %T %N Total Reads At Index 59 | 0 100.00 0.00 0.00 0.00 0.00 20 60 | 1 5.26 94.74 0.00 0.00 0.00 19 61 | 2 5.26 0.00 0.00 94.74 0.00 19 62 | 3 0.00 0.00 94.44 0.00 5.56 18 63 | 4 50.00 38.89 0.00 0.00 11.11 18 64 | 5 52.94 47.06 0.00 0.00 0.00 17 65 | 6 0.00 50.00 0.00 50.00 0.00 18 66 | 7 0.00 0.00 38.89 11.11 50.00 18 67 | 8 44.44 0.00 5.56 0.00 50.00 18 68 | 9 0.00 88.24 11.76 0.00 0.00 17 69 | 10 11.11 0.00 0.00 88.89 0.00 9 70 | 11 0.00 0.00 0.00 0.00 100.00 8 71 | 12 0.00 0.00 100.00 0.00 0.00 8 72 | 13 100.00 0.00 0.00 0.00 0.00 4 73 | 14 33.33 66.67 0.00 0.00 0.00 3 74 | 15 0.00 33.33 0.00 66.67 0.00 3 75 | 16 0.00 0.00 100.00 0.00 0.00 2 76 | 17 100.00 0.00 0.00 0.00 0.00 2 77 | 18 0.00 100.00 0.00 0.00 0.00 2 78 | 19 0.00 0.00 0.00 100.00 0.00 2 79 | 20 0.00 0.00 0.00 0.00 100.00 2 80 | 21 100.00 0.00 0.00 0.00 0.00 2 81 | 22 0.00 100.00 0.00 0.00 0.00 2 82 | 23 0.00 0.00 0.00 100.00 0.00 2 83 | 24 0.00 0.00 0.00 0.00 100.00 2 84 | 25 0.00 0.00 100.00 0.00 0.00 2 85 | 86 | Finished processing testFile.txt with 95 lines containing 21 sequences. 87 | There were a total of 47 errors. 88 | Returning: 1 : FASTQ_INVALID 89 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsNoBaseComp.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition, --avgQual, --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace [ON], --colorSpace, --auto 7 | Errors : --ignoreErrors, --printableErrors [100] 8 | 9 | ERROR on Line 2: Invalid character ('.') in base sequence. 10 | ERROR on Line 2: Invalid character ('0') in base sequence. 11 | ERROR on Line 2: Invalid character ('1') in base sequence. 12 | ERROR on Line 2: Invalid character ('2') in base sequence. 13 | ERROR on Line 2: Invalid character ('3') in base sequence. 14 | ERROR on Line 11: Invalid character ('1') in base sequence. 15 | ERROR on Line 11: Invalid character ('2') in base sequence. 16 | ERROR on Line 11: Invalid character ('3') in base sequence. 17 | ERROR on Line 11: Invalid character ('.') in base sequence. 18 | ERROR on Line 11: Invalid character ('0') in base sequence. 19 | ERROR on Line 11: Invalid character ('3') in base sequence. 20 | ERROR on Line 11: Invalid character ('2') in base sequence. 21 | ERROR on Line 11: Invalid character ('1') in base sequence. 22 | ERROR on Line 11: Invalid character ('.') in base sequence. 23 | ERROR on Line 11: Invalid character ('0') in base sequence. 24 | ERROR on Line 11: Invalid character ('1') in base sequence. 25 | ERROR on Line 11: Invalid character ('1') in base sequence. 26 | ERROR on Line 25: The sequence identifier line was too short. 27 | ERROR on Line 29: First line of a sequence does not begin with @ 28 | ERROR on Line 33: No Sequence Identifier specified before the comment. 29 | ERROR on Line 37: No Sequence Identifier specified before the comment. 30 | ERROR on Line 41: Repeated Sequence Identifier: Valid at Lines 1 and 41 31 | ERROR on Line 46: Invalid character ('H') in base sequence. 32 | ERROR on Line 46: Invalid character ('0') in base sequence. 33 | ERROR on Line 47: Invalid character ('B') in base sequence. 34 | ERROR on Line 47: Invalid character ('Z') in base sequence. 35 | ERROR on Line 52: Raw Sequence is shorter than the min read length: 3 < 10 36 | ERROR on Line 56: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 37 | ERROR on Line 57: Looking for continuation of Raw Sequence or '+' instead found a blank line, assuming it was part of Raw Sequence. 38 | ERROR on Line 63: Invalid character (' ') in quality string. 39 | ERROR on Line 64: Invalid character (' ') in quality string. 40 | ERROR on Line 77: Quality string length (12) does not equal raw sequence length (10) 41 | ERROR on Line 88: Sequence Identifier on '+' line does not equal the one on the '@' line. 42 | ERROR on Line 91: Invalid character ('0') in base sequence. 43 | ERROR on Line 91: Invalid character ('1') in base sequence. 44 | ERROR on Line 91: Invalid character ('2') in base sequence. 45 | ERROR on Line 91: Invalid character ('3') in base sequence. 46 | ERROR on Line 91: Invalid character ('.') in base sequence. 47 | ERROR on Line 91: Invalid character ('0') in base sequence. 48 | ERROR on Line 91: Invalid character ('3') in base sequence. 49 | ERROR on Line 91: Invalid character ('2') in base sequence. 50 | ERROR on Line 91: Invalid character ('1') in base sequence. 51 | ERROR on Line 91: Invalid character ('.') in base sequence. 52 | ERROR on Line 91: Invalid character ('0') in base sequence. 53 | ERROR on Line 91: Invalid character ('1') in base sequence. 54 | ERROR on Line 91: Invalid character ('1') in base sequence. 55 | ERROR on Line 95: Reached the end of the file without a '+' line. 56 | ERROR on Line 95: Incomplete Sequence, missing Quality String. 57 | Finished processing testFile.txt with 95 lines containing 21 sequences. 58 | There were a total of 48 errors. 59 | Returning: 1 : FASTQ_INVALID 60 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsNoBaseCompNoErrors.txt: -------------------------------------------------------------------------------- 1 | 2 | Input Parameters 3 | --file [testFile.txt], --baseComposition, --avgQual [ON], --disableSeqIDCheck, 4 | --interleaved, --noeof, --quiet, --params [ON], 5 | --minReadLen [10], --maxErrors [-1] 6 | Space Type : --baseSpace [ON], --colorSpace, --auto 7 | Errors : --ignoreErrors [ON], --printableErrors 8 | 9 | 10 | Average Phred Quality by Read Index (starts at 0): 11 | Read Index Average Quality 12 | 0 44.10 13 | 1 45.55 14 | 2 51.11 15 | 3 47.68 16 | 4 47.37 17 | 5 43.63 18 | 6 48.37 19 | 7 48.47 20 | 8 53.28 21 | 9 50.00 22 | 10 52.62 23 | 11 49.69 24 | 12 51.08 25 | 13 47.20 26 | 14 45.75 27 | 15 57.67 28 | 16 72.00 29 | 17 73.00 30 | 18 74.00 31 | 19 75.00 32 | 20 47.50 33 | 21 77.00 34 | 22 78.00 35 | 23 79.00 36 | 24 80.00 37 | 25 80.50 38 | 39 | Overall Average Phred Quality = 50.40 40 | Finished processing testFile.txt with 95 lines containing 21 sequences. 41 | There were a total of 48 errors. 42 | Returning: 1 : FASTQ_INVALID 43 | -------------------------------------------------------------------------------- /test/expectedResults/ExpectedResultsTestFile2.txt: -------------------------------------------------------------------------------- 1 | Finished processing testFile2.txt with 20 lines containing 4 sequences. 2 | There were a total of 0 errors. 3 | Returning: 0 : FASTQ_SUCCESS 4 | -------------------------------------------------------------------------------- /test/interleaved.fastq: -------------------------------------------------------------------------------- 1 | @1 1 2 | GGGAAATTTCCCTTTGGGAAAGGG 3 | + 4 | 325wregkl90923<>><><>,.< 5 | @1 2 6 | CCCTTTCCCAAAGGGAAATTTCCC 7 | + 8 | <.,><><>><32909lkgerw523 9 | @2/1 10 | GGGAAATTTCCCTTTGGGAAAGGG 11 | + 12 | 325wregkl90923<>><><>,.< 13 | @2/2 14 | CCCCTTTCCCAAAGGGAAATTCCC 15 | + 16 | <.,><><>><32909lkgerw523 17 | @3/1 18 | GGGAAATTTCCCTTTGGGAAAGGG 19 | + 20 | 325wregkl90923<>><><>,.< 21 | @3/3 22 | CCCCTTTCCCAAAGGGAAATTCCC 23 | + 24 | <.,><><>><32909lkgerw523 25 | @4 26 | GGGAAATTTCCCTTTGGGAAAGGG 27 | + 28 | 325wregkl90923<>><><>,.< 29 | @4 30 | CCCCTTTCCCAAAGGGAAATTCCC 31 | + 32 | <.,><><>><32909lkgerw523 33 | @5/1 34 | GGGAAATTTCCCTTTGGGAAAGGG 35 | + 36 | 325waegkl90923<>><><>,.< 37 | @5 38 | CCCTTTCCCAAAGGGAAATTTCCC 39 | + 40 | <.,><><>><32909lkgerw523 41 | @6/1 42 | GGGAAATTTCCCTTTGGGAAAGGG 43 | + 44 | 325wregkl90923<>><><>,.< 45 | @6/2 46 | CCCTTTCCCAAAGGGAAATTTCCC 47 | + 48 | <.,><><>><32909lkgeaw523 49 | @7/1 50 | GGGAAATTTCCCTTTGGGAAAGGG 51 | + 52 | <>,.><><>,-< 53 | @7/2 54 | CCCTTTCCCAAAGGGAAATTTCCC 55 | + 56 | ,><><>><32908lkge<.<.523 57 | -------------------------------------------------------------------------------- /test/testFile.txt.bgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/statgen/fastQValidator/6d619a34749e9d33c34ef0d3e0e87324ca77f320/test/testFile.txt.bgz -------------------------------------------------------------------------------- /test/testFile.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/statgen/fastQValidator/6d619a34749e9d33c34ef0d3e0e87324ca77f320/test/testFile.txt.gz -------------------------------------------------------------------------------- /test/testFile.txt.noeof.bgz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/statgen/fastQValidator/6d619a34749e9d33c34ef0d3e0e87324ca77f320/test/testFile.txt.noeof.bgz -------------------------------------------------------------------------------- /test/testFile2.txt: -------------------------------------------------------------------------------- 1 | @Valid with comment 2 | ACTGNactngnactg 3 | + 4 | !#"$%&'()*+,-./ 5 | @Valid1 with comment 6 | ACTGACTNactngaac 7 | + 8 | 0123456789:;<=> 9 | @ 10 | @Valid3 11 | ACTGACTN 12 | actngACTGACTNactng 13 | + 14 | LMNOPQRSTUVWXYZ 15 | [\]^_'abcde 16 | @Valid4 17 | ACTGACTNactng 18 | ACTGACTNactng 19 | + 20 | fghijklmnopqrstuvwxyz{|}~~ 21 | 22 | --------------------------------------------------------------------------------