├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── all.fa.gz ├── bin ├── Linux_x86_64_kernel_3.10.0 │ └── quack ├── MacOS_10.14.6 │ └── quack └── Windows_Cygwin_2.904_x86_64 │ └── quack.exe ├── images ├── .gitignore ├── explanation.overlay.svg ├── explanation.png ├── makefile ├── paired.adapter.png ├── paired.adapter.svg ├── paired.noadapt.png ├── paired.noadapt.svg ├── single.adapter.png ├── single.adapter.svg ├── single.noadapt.png └── single.noadapt.svg ├── makefile ├── quack.c ├── svg.c └── svg.h /.gitignore: -------------------------------------------------------------------------------- 1 | *~ 2 | *.o 3 | quack 4 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 1 | [submodule "klib"] 2 | path = klib 3 | url = https://github.com/attractivechaos/klib 4 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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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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 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 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 | {project} Copyright (C) {year} {fullname} 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 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # quack 2 | 3 | A FASTQ quality assessment tool 4 | 5 | ## Citation 6 | A. Thrash, M. Arick, and D. G. Peterson, “Quack: A quality assurance tool for high throughput sequence data,” Analytical Biochemistry, vol. 548, pp. 38–43, 2018. https://doi.org/10.1016/j.ab.2018.01.028 7 | 8 | ## Latest Release 9 | 10 | The latest release of quack and its binaries can always be found [here](https://github.com/IGBB/quack/releases/latest). 11 | 12 | ## Dependencies 13 | 14 | * zlib 15 | * klib (pulled by the submodule update below) 16 | 17 | ## Installation from Source 18 | 19 | git clone https://github.com/IGBB/quack.git 20 | 21 | cd quack/ 22 | 23 | make && make test 24 | 25 | ## Binaries 26 | 27 | Binaries are available in the bin/ folder. Current testing of these binaries has been limited. If a binary doesn't work, try compiling from source on your system. 28 | 29 | ## Running Quack 30 | 31 | Quack has the following options. 32 | 33 | ``` 34 | -1, --forward forward strand data in gzipped FASTQ format, must be used with -2 or --reverse 35 | -2, --reverse reverse strand data in gzipped FASTQ format, must be used with -1 or --forward 36 | -a, --adapters adapters in gzipped FASTA format (optional) 37 | -n, --name a descriptive name to be printed with the output image (optional) 38 | -u, --unpaired unpaired data in gzipped FASTQ format 39 | -?, --help, --usage prints the help or usage information 40 | -V, --version prints the program version 41 | ``` 42 | 43 | Quack takes gzipped FASTQ-formatted files as input for data and gzipped As output, quack prints an SVG formatted image to standard output. 44 | 45 | 46 | ### Examples 47 | 48 | #### Paired-end with name and adapters 49 | `quack -1 reads.1.fastq.gz -2 reads.2.fastq.gz -n sample_name -a adapters_files.fasta.gz > sample_name.svg` 50 | 51 | #### Unpaired with name and adapters 52 | `quack -u reads.fastq.gz -n sample_name -a adapters.fa.gz > sample_name.svg` 53 | 54 | #### Paired-end without name and adapters 55 | `quack -1 reads.1.fastq.gz -2 reads.2.fastq.gz > sample_name.svg` 56 | 57 | #### Unpaired without name and adapters 58 | `quack -u reads.fastq.gz > sample_name.svg` 59 | 60 | ### Output 61 | 62 | Quack is capable of producing output for single-ended data and paired-end data. Only the singled-ended data is labeled, since the paried-end data has all the same parts. 63 | 64 | #### Single-ended Data 65 | ![explanation](images/explanation.png) 66 | 67 | 68 | A. The base content distribution showing the percentage of each nucleotide in each column of an array. 69 | B. A heatmap showing the distribution of sequence quality for each column and a line representing mean quality scores across the array 70 | C. A score distribution graph showing the percentage of bases matching certain scores, with 100% on the left of the graph and 0% on the right. The highest scoring data appears at the top of the graph. 71 | D. Length distribution graph showing the percentage of reads of a given length 72 | E. Adapter content distribution graph showing how adapter content is distributed throughout an array 73 | 74 | #### Paired-end Data 75 | ![paired](images/paired.adapter.png) 76 | -------------------------------------------------------------------------------- /all.fa.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/all.fa.gz -------------------------------------------------------------------------------- /bin/Linux_x86_64_kernel_3.10.0/quack: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/bin/Linux_x86_64_kernel_3.10.0/quack -------------------------------------------------------------------------------- /bin/MacOS_10.14.6/quack: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/bin/MacOS_10.14.6/quack -------------------------------------------------------------------------------- /bin/Windows_Cygwin_2.904_x86_64/quack.exe: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/bin/Windows_Cygwin_2.904_x86_64/quack.exe -------------------------------------------------------------------------------- /images/.gitignore: -------------------------------------------------------------------------------- 1 | SRR1168757.fastq.gz 2 | ERR1438847_1.fastq.gz 3 | ERR1438847_2.fastq.gz 4 | -------------------------------------------------------------------------------- /images/explanation.overlay.svg: -------------------------------------------------------------------------------- 1 | 2 | A 4 | B 6 | C 8 | D 10 | E 12 | 13 | -------------------------------------------------------------------------------- /images/explanation.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/images/explanation.png -------------------------------------------------------------------------------- /images/makefile: -------------------------------------------------------------------------------- 1 | 2 | SRR1168757.fastq.gz: 3 | wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR116/007/SRR1168757/$@ 4 | 5 | ERR1438847_%.fastq.gz: 6 | wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR143/007/ERR1438847/$@ 7 | 8 | single.adapter.svg : ../quack SRR1168757.fastq.gz 9 | ../quack -u SRR1168757.fastq.gz -a ../all.fa.gz -n SRR1168757 > $@ 10 | 11 | single.noadapt.svg : ../quack SRR1168757.fastq.gz 12 | ../quack -u SRR1168757.fastq.gz -n SRR1168757 > $@ 13 | 14 | paired.adapter.svg : ../quack ERR1438847_1.fastq.gz ERR1438847_2.fastq.gz 15 | ../quack -1 ERR1438847_1.fastq.gz -2 ERR1438847_2.fastq.gz -a ../all.fa.gz -n ERR1438847 > $@ 16 | 17 | paired.noadapt.svg : ../quack ERR1438847_1.fastq.gz ERR1438847_2.fastq.gz 18 | ../quack -1 ERR1438847_1.fastq.gz -2 ERR1438847_2.fastq.gz -n ERR1438847 > $@ 19 | 20 | explanation.overlay.png : explanation.overlay.svg 21 | convert -background none $< $@ 22 | 23 | explanation.png : explanation.overlay.png single.adapter.png 24 | composite -gravity center $^ $@ 25 | 26 | %.png: %.svg 27 | convert $< $@ 28 | 29 | .PHONY: clean all 30 | clean: 31 | rm -f $(obj) quack ERR1438847_1.fastq.gz ERR1438847_2.fastq.gz 32 | 33 | all: paired.adapter.png \ 34 | paired.noadapt.png \ 35 | single.adapter.png \ 36 | single.noadapt.png \ 37 | explanation.png 38 | -------------------------------------------------------------------------------- /images/paired.adapter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/images/paired.adapter.png -------------------------------------------------------------------------------- /images/paired.noadapt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/images/paired.noadapt.png -------------------------------------------------------------------------------- /images/single.adapter.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/images/single.adapter.png -------------------------------------------------------------------------------- /images/single.noadapt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/IGBB/quack/cf394194d22884e26ba470c0442aaf83a0f8a842/images/single.noadapt.png -------------------------------------------------------------------------------- /images/single.noadapt.svg: -------------------------------------------------------------------------------- 1 | 2 | 3 | SRR1168757 4 | 5 | 6 | 7 | 4000000 8 | 9 | reads with endcoding 10 | 11 | phred33 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | Base Content Percentage 42 | 43 | 44 | %A 45 | 46 | %T 47 | 48 | %C 49 | 50 | %G 51 | 52 | Percent 53 | 54 | 55 | 0 56 | 57 | 58 | 100 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | 119 | 120 | 121 | 122 | 123 | 124 | 125 | 126 | 127 | 128 | 129 | 130 | 131 | 132 | 133 | 134 | 135 | 136 | 137 | 138 | 139 | 140 | 141 | 142 | 143 | 144 | 145 | 146 | 147 | 148 | 149 | 150 | 151 | 152 | 153 | 154 | 155 | 156 | 157 | 158 | 159 | 160 | 161 | 162 | 163 | 164 | 165 | 166 | 167 | 168 | 169 | 170 | 171 | 172 | 173 | 174 | 175 | 176 | 177 | 178 | 179 | 180 | 181 | 182 | 183 | 184 | 185 | 186 | 187 | 188 | 189 | 190 | 191 | 192 | 193 | 194 | 195 | 196 | 197 | 198 | 199 | 200 | 201 | 202 | 203 | 204 | 205 | 206 | 207 | 208 | 209 | 210 | 211 | 212 | 213 | 214 | 215 | 216 | 217 | 218 | 219 | 220 | 221 | 222 | 223 | 224 | 225 | 226 | 227 | 228 | 229 | 230 | 231 | 232 | 233 | 234 | 235 | 236 | 237 | 238 | 239 | 240 | 241 | 242 | 243 | 244 | 245 | 246 | 247 | 248 | 249 | 250 | 251 | 252 | 253 | 254 | 255 | 256 | 257 | 258 | 259 | 260 | 261 | 262 | 263 | 264 | 265 | 266 | 267 | 268 | 269 | 270 | 271 | 272 | 273 | 274 | 275 | 276 | 277 | 278 | 279 | 280 | 281 | 282 | 283 | 284 | 285 | 286 | 287 | 288 | 289 | 290 | 291 | 292 | 293 | 294 | 295 | 296 | 297 | 298 | 299 | 300 | 301 | 302 | 303 | 304 | 305 | 306 | 307 | 308 | 309 | 310 | 311 | 312 | 313 | 314 | 315 | 316 | 317 | 318 | 319 | 320 | 321 | 322 | 323 | 324 | 325 | 326 | 327 | 328 | 329 | 330 | 331 | 332 | 333 | 334 | 335 | 336 | 337 | 338 | 339 | 340 | 341 | 342 | 343 | 344 | 345 | 346 | 347 | 348 | 349 | 350 | 351 | 352 | 353 | 354 | 355 | 356 | 357 | 358 | 359 | 360 | 361 | 362 | 363 | 364 | 365 | 366 | 367 | 368 | 369 | 370 | 371 | 372 | 373 | 374 | 375 | 376 | 377 | 378 | 379 | 380 | 381 | 382 | 383 | 384 | 385 | 386 | 387 | 388 | 389 | 390 | 391 | 392 | 393 | 394 | 395 | 396 | 397 | 398 | 399 | 400 | 401 | 402 | 403 | 404 | 405 | 406 | 407 | 408 | 409 | 410 | 411 | 412 | 413 | 414 | 415 | 416 | 417 | 418 | 419 | 420 | 421 | 422 | 423 | 424 | 425 | 426 | 427 | 428 | 429 | 430 | 431 | 432 | 433 | 434 | 435 | 436 | 437 | 438 | 439 | 440 | 441 | 442 | 443 | 444 | 445 | 446 | 447 | 448 | 449 | 450 | 451 | 452 | 453 | 454 | 455 | 456 | 457 | 458 | 459 | 460 | 461 | 462 | 463 | 464 | 465 | 466 | 467 | 468 | 469 | 470 | 471 | 472 | 473 | 474 | 475 | 476 | 477 | 478 | 479 | 480 | 481 | 482 | 483 | 484 | 485 | 486 | 487 | 488 | 489 | 490 | 491 | 492 | 493 | 494 | 495 | 496 | 497 | 498 | 499 | 500 | 501 | 502 | 503 | 504 | 505 | 506 | 507 | 508 | 509 | 510 | 511 | 512 | 513 | 514 | 515 | 516 | 517 | 518 | 519 | 520 | 521 | 522 | 523 | 524 | 525 | 526 | 527 | 528 | 529 | 530 | 531 | 532 | 533 | 534 | 535 | 536 | 537 | 538 | 539 | 540 | 541 | 542 | 543 | 544 | 545 | 546 | 547 | 548 | 549 | 550 | 551 | 552 | 553 | 554 | 555 | 556 | 557 | 558 | 559 | 560 | 561 | 562 | 563 | 564 | 565 | 566 | 567 | 568 | 569 | 570 | 571 | 572 | 573 | 574 | 575 | 576 | 577 | 578 | 579 | 580 | 581 | 582 | 583 | 584 | 585 | 586 | 587 | 588 | 589 | 590 | 591 | 592 | 593 | 594 | 595 | 596 | 597 | 598 | 599 | Per Base Sequence Quality 600 | 601 | 602 | 42 603 | 604 | 28 605 | 606 | 20 607 | 608 | 609 | 610 | 611 | 612 | Length Distribution 613 | 614 | 615 | Percent 616 | 617 | 618 | 0 619 | 620 | 621 | 100 622 | 623 | 624 | Base Pairs 625 | 626 | 627 | 0 628 | 629 | 630 | 100 631 | 632 | 633 | 634 | 635 | 636 | 637 | 638 | 639 | 640 | 641 | 642 | 643 | 644 | 645 | 646 | 647 | 648 | 649 | 650 | 651 | 652 | 653 | 654 | 655 | Score 656 | 657 | 658 | Distribution 659 | 660 | 661 | 662 | Percent 663 | 664 | 665 | 100 666 | 667 | 668 | Score 669 | 670 | 671 | 42 672 | 673 | 674 | 1 675 | 676 | 677 | 678 | 679 | -------------------------------------------------------------------------------- /makefile: -------------------------------------------------------------------------------- 1 | src = $(wildcard *.c) 2 | obj = $(src:.c=.o) 3 | 4 | override LDFLAGS := -lz -lm $(LDFLAGS) 5 | override CFLAGS := -Iklib -O3 $(CFLAGS) 6 | 7 | all : klib/kseq.h quack 8 | 9 | quack: $(obj) 10 | $(CC) -o $@ $^ $(LDFLAGS) 11 | 12 | klib/kseq.h: 13 | git submodule update --init --recursive 14 | 15 | %.o: %.c 16 | $(CC) $(CFLAGS) -o $@ -c $< 17 | 18 | .PHONY: all clean images test 19 | clean: 20 | rm -f $(obj) quack 21 | 22 | images: quack 23 | $(MAKE) -C images all 24 | 25 | test: images 26 | -------------------------------------------------------------------------------- /quack.c: -------------------------------------------------------------------------------- 1 | #include 2 | #include 3 | #include 4 | #include 5 | #include 6 | #include 7 | 8 | #include "kseq.h" 9 | #include "svg.h" 10 | 11 | #define unlikely(x) __builtin_expect ((x), 0) 12 | #define likely(x) __builtin_expect((x),1) 13 | 14 | 15 | #define svg_axis_label( posx, posy, rot, label) \ 16 | svg_start_tag("text", 7, \ 17 | svg_attr("x", "%d", posx), \ 18 | svg_attr("fill", "%s", "#AAA"), \ 19 | svg_attr("y", "%d", posy), \ 20 | svg_attr("font-family", "%s", "sans-serif"), \ 21 | svg_attr("font-size", "%s", "15px"), \ 22 | svg_attr("text-anchor", "%s", "middle"), \ 23 | svg_attr("transform", "rotate(%d)", rot) \ 24 | ); \ 25 | printf("%s\n", label); \ 26 | svg_end_tag("text"); 27 | #define svg_axis_number( posx, posy, a, number) \ 28 | svg_start_tag("text", 6, \ 29 | svg_attr("x", "%d", posx), \ 30 | svg_attr("fill", "%s", "#AAA"), \ 31 | svg_attr("y", "%d", posy), \ 32 | svg_attr("font-family", "%s", "sans-serif"), \ 33 | svg_attr("font-size", "%s", "10px"), \ 34 | svg_attr("text-anchor", "%s", a) \ 35 | ); \ 36 | printf("%d\n", number); \ 37 | svg_end_tag("text"); 38 | 39 | #define svg_center_label( posx, posy, fillv, label_format, label) \ 40 | svg_start_tag("text", 7, \ 41 | svg_attr("x", "%d", posx), \ 42 | svg_attr("y", "%d", posy), \ 43 | svg_attr("fill", "%s", fillv), \ 44 | svg_attr("font-family", "%s", "sans-serif"), \ 45 | svg_attr("font-size", "%s", "15px"), \ 46 | svg_attr("font-weight", "%s", "bold"), \ 47 | svg_attr("text-anchor", "%s", "middle") \ 48 | ); \ 49 | printf(label_format, label); \ 50 | svg_end_tag("text"); 51 | 52 | 53 | 54 | const char *program_version = "quack 1.1.1"; 55 | struct arguments { 56 | char *name, *forward, *reverse, *unpaired, *adapters; 57 | }; 58 | 59 | struct arguments parse_options(int argc, char **argv) { 60 | struct arguments arguments = { 61 | .unpaired = NULL, 62 | .forward = NULL, 63 | .reverse = NULL, 64 | .name = NULL, 65 | .adapters = NULL 66 | }; 67 | 68 | if (argc== 1 || argc == 2) { 69 | if (argc == 1 || (strcmp(argv[1], "--help") == 0 || strcmp(argv[1], "--usage") == 0 || strcmp(argv[1], "-?") == 0)) { 70 | printf("Usage: quack [OPTION...]\n" 71 | "quack -- A FASTQ quality assessment tool\n\n" 72 | " -1, --forward file.1.fq.gz Forward strand\n" 73 | " -2, --reverse file.2.fq.gz Reverse strand\n" 74 | " -a, --adapters adapters.fa.gz (Optional) Adapters file\n" 75 | " -n, --name NAME (Optional) Display in output\n" 76 | " -u, --unpaired unpaired.fq.gz Data (only use with -u)\n" 77 | " -?, --help Give this help list\n" 78 | " --usage (use alone)\n" 79 | " -V, --version Print program version (use alone)\n" 80 | "Report bugs to .\n"); 81 | } 82 | 83 | if (argc == 2 && ((strcmp(argv[1], "-V") == 0 || strcmp(argv[1], "--version") == 0))) { 84 | printf("%s\n", program_version); 85 | exit (0); 86 | } 87 | } 88 | 89 | if(argc>2 && argc % 2 != 0) 90 | { 91 | int counter=1; 92 | while (counter.\n"); 124 | 125 | exit(EXIT_FAILURE); 126 | } 127 | 128 | counter = counter+2; 129 | } 130 | } 131 | return arguments; 132 | } 133 | 134 | typedef struct { 135 | uint64_t scores[91]; 136 | uint64_t content[4]; 137 | uint64_t length_count; 138 | uint64_t kmer_count; 139 | } base_information; 140 | 141 | typedef struct { 142 | base_information *bases; 143 | uint64_t max_length; 144 | uint64_t original_max_length; 145 | uint64_t number_of_sequences; 146 | } sequence_data; 147 | 148 | /* Convert ASCII to Integer for A T C and G */ 149 | /* A C G T */ 150 | int lookup[20] = {0, 0, 2, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1}; 151 | 152 | KSEQ_INIT(gzFile, gzread) 153 | 154 | int* read_adapters(char *adapters_file) { 155 | int kmer_size = 10; 156 | int array_size = pow(4, kmer_size); 157 | gzFile fp; 158 | kseq_t *seq; 159 | int i, l, index; 160 | fp = gzopen(adapters_file, "r"); 161 | seq = kseq_init(fp); 162 | int *kmers = malloc(array_size*sizeof(int)); 163 | memset(kmers, 0, array_size*sizeof(int)); 164 | while ((l = kseq_read(seq)) >= 0) { 165 | index = 0; 166 | for (i = 0; i < kmer_size; i++) { 167 | index = ((index << 2) + (lookup[seq->seq.s[i]-65 & ~32])) & (array_size-1); 168 | } 169 | for (; i < seq->seq.l; i++) { 170 | index = ((index << 2) + (lookup[seq->seq.s[i]-65 & ~32])) & (array_size-1); 171 | kmers[index] = 1; 172 | } 173 | 174 | } 175 | kseq_destroy(seq); 176 | gzclose(fp); 177 | return kmers; 178 | } 179 | 180 | sequence_data* read_fastq(char *fastq_file, int *kmers) { 181 | gzFile fp; 182 | kseq_t *seq; 183 | int i, l, index; 184 | int kmer_size = 10; 185 | int array_size = pow(4, kmer_size); 186 | int max_length = 0; 187 | fp = gzopen(fastq_file, "r"); 188 | seq = kseq_init(fp); 189 | base_information *bases = NULL; 190 | sequence_data *to_return = malloc(sizeof(sequence_data)); 191 | int number_of_sequences = 0; 192 | 193 | while ((l = kseq_read(seq)) >= 0) { 194 | if (unlikely(seq->seq.l > max_length)) { 195 | bases = realloc(bases, seq->seq.l*sizeof(base_information)); 196 | memset(bases+max_length, 0, (seq->seq.l - max_length)*sizeof(base_information)); 197 | max_length = seq->seq.l; 198 | } 199 | for (i = 0; i < seq->seq.l; i++) { 200 | int base = seq->seq.s[i]; 201 | int offset = lookup[base-65 & ~32]; 202 | bases[i].content[offset]++; 203 | int quality = seq->qual.s[i]-33; 204 | bases[i].scores[quality]++; 205 | } 206 | index = 0; 207 | for (i = 0; i < kmer_size; i++) { 208 | index = ((index << 2) + (lookup[seq->seq.s[i]-65 & ~32])) & (array_size-1); 209 | } 210 | if (kmers) { 211 | for (; kmers[index] == 0 && i < seq->seq.l; i++) { 212 | index = ((index << 2) + (lookup[seq->seq.s[i]-65 & ~32])) & (array_size-1); 213 | } 214 | } 215 | if (i < seq->seq.l) { 216 | bases[i].kmer_count++; 217 | } 218 | 219 | bases[seq->seq.l-1].length_count++; 220 | number_of_sequences++; 221 | } 222 | kseq_destroy(seq); 223 | gzclose(fp); 224 | to_return->bases = bases; 225 | to_return->max_length = max_length; 226 | to_return->number_of_sequences = number_of_sequences; 227 | return to_return; 228 | } 229 | 230 | sequence_data* transform(sequence_data* data) { 231 | int i, j; 232 | data->original_max_length = data->max_length; 233 | // binning 234 | if (data->max_length > 3000) { 235 | fprintf(stderr, "Binning...\n"); 236 | int bin_size = 100; 237 | int unbinned; 238 | int binned = 0; 239 | 240 | for (unbinned = 1; unbinned < data->max_length; unbinned++) { 241 | if (unbinned%bin_size == 0){ 242 | binned++; 243 | for (i = 0; i < 4; i++) { 244 | data->bases[binned].content[i] = 0; 245 | } 246 | for (i = 0; i < 91; i++) { 247 | data->bases[binned].scores[i] = 0; 248 | } 249 | data->bases[binned].length_count = 0; 250 | } 251 | for (i = 0; i < 4; i++) { 252 | data->bases[binned].content[i] = data->bases[binned].content[i] + data->bases[unbinned].content[i]; 253 | } 254 | for (i = 0; i < 91; i++) { 255 | data->bases[binned].scores[i] = data->bases[binned].scores[i] + data->bases[unbinned].scores[i]; 256 | } 257 | // fprintf(stderr, "%d\n", data->bases[binned].length_count); 258 | data->bases[binned].length_count = data->bases[binned].length_count + data->bases[unbinned].length_count; 259 | data->bases[binned].kmer_count = data->bases[binned].kmer_count + data->bases[unbinned].kmer_count; 260 | } 261 | data->max_length = binned; 262 | } 263 | 264 | for (i = 1; i < data->max_length; i++) { 265 | data->bases[i].kmer_count = data->bases[i-1].kmer_count + data->bases[i].kmer_count; 266 | } 267 | 268 | // transforming data for drawing (percentages rather than counts) 269 | for (i = 0; i < data->max_length; i++) { 270 | int content_sum = 0; 271 | int score_sum = 0; 272 | /* for (j = 0; j < 4; j++) { */ 273 | /* content_sum = content_sum + data->bases[i].content[j]; */ 274 | /* } */ 275 | /* if (content_sum != 0) { */ 276 | /* for (j = 0; j < 4; j++) { */ 277 | /* data->bases[i].content[j] = 100*data->bases[i].content[j]/content_sum; */ 278 | /* } */ 279 | /* } */ 280 | for (j = 0; j < 91; j++) { 281 | score_sum = score_sum + data->bases[i].scores[j]; 282 | } 283 | if (score_sum != 0) { 284 | for (j = 0; j < 91; j++) { 285 | data->bases[i].scores[j] = 100*data->bases[i].scores[j]/score_sum; 286 | } 287 | } 288 | data->bases[i].length_count = ceil(100*(float)data->bases[i].length_count/data->number_of_sequences); 289 | data->bases[i].kmer_count = ceil(100*(float)data->bases[i].kmer_count/(float)data->number_of_sequences); 290 | 291 | } 292 | return data; 293 | } 294 | 295 | void draw(sequence_data* data, int position, int adapters_used) { 296 | int i, j, x, y; 297 | int counter = 0; 298 | int max_score = 0; 299 | uint64_t number_of_bases = 0; 300 | uint64_t total_counts[91] = {0}; 301 | float averages[500]; 302 | 303 | /********** Get Encoding ***************/ 304 | char *encoding = "phred64"; 305 | int offset = 31; 306 | /* Loop through every base */ 307 | for( i=0; i < data->max_length; i++ ){ 308 | 309 | /* Loop through scores, breaking when first non-zero is found for current 310 | * base */ 311 | for(j=0; j < 31; j++){ 312 | if(data->bases[i].scores[j] > 0) break; 313 | } 314 | 315 | /* Found encoding if j is lower than 31 (lower than possible for phred64 316 | * encoding) */ 317 | if(j < 31){ 318 | encoding="phred33"; 319 | offset=0; 320 | break; 321 | } 322 | } 323 | 324 | 325 | // get max score, score distribution, and average scores at each position 326 | max_score = 40; 327 | for (i = 0; i < data->max_length; i++) { 328 | int sum = 0; 329 | for (j = offset; j < 91; j++) { 330 | if (data->bases[i].scores[j] > 0 && (j-offset) > max_score) { 331 | max_score = j - offset; 332 | } 333 | total_counts[j - offset] += data->bases[i].scores[j]; 334 | sum += (j - offset)*data->bases[i].scores[j]; 335 | 336 | } 337 | number_of_bases ++; 338 | /* score counts are already converted to percentage of total counts; so, all 339 | * that needs to be done to find average is divide by 100 */ 340 | averages[i] = sum/100.0; 341 | } 342 | 343 | 344 | /********** File Stats ***************/ 345 | svg_start_tag("text", 6, 346 | svg_attr("x", "%d", (position==0)?355:835), 347 | svg_attr("y", "%d", 20), 348 | svg_attr("text-anchor", "%s", "middle"), 349 | svg_attr("font-family", "%s", "sans-serif"), 350 | svg_attr("font-size", "%s", "15px"), 351 | svg_attr("fill", "%s", "#555") 352 | ); 353 | svg_start_tag("tspan", 0); 354 | printf("%d", data->number_of_sequences); 355 | svg_end_tag("tspan"); 356 | svg_start_tag("tspan", 1, svg_attr("fill", "%s", "#888")); 357 | printf(" reads with endcoding "); 358 | svg_end_tag("tspan"); 359 | svg_start_tag("tspan", 0); 360 | printf("%s", encoding); 361 | svg_end_tag("tspan"); 362 | svg_end_tag("text"); 363 | 364 | /* Group for rug plot */ 365 | svg_start_tag("g", 1, 366 | svg_attr("transform", "translate(%d %d)", 5, 25) 367 | ); 368 | 369 | /* Horizontal Tick marks */ 370 | x = 100; 371 | if (position==1) 372 | x = 1000; 373 | for (i = 10; i < 100; i+=10){ 374 | y = 105 + i * 250 / 100; 375 | 376 | svg_simple_tag("line",6, 377 | svg_attr("x1", "%d", x), 378 | svg_attr("x2", "%d", x+100), 379 | svg_attr("y1", "%d", y), 380 | svg_attr("y2", "%d", y), 381 | svg_attr("stroke", "%s", "black"), 382 | svg_attr("stroke-width", "%f", (i%20 == 10)?1:0.5) 383 | ); 384 | } 385 | 386 | 387 | /* Group for the vertical section of rug plot */ 388 | svg_start_tag("g", 1, 389 | svg_attr("transform", "translate(%d 0)", (position == 1)?610:130) 390 | ); 391 | 392 | 393 | /*************** Vertical Tick Marks ***************/ 394 | y = (adapters_used == 0)?400:500; 395 | for (i = 10; i < 100; i+=10){ 396 | x = i * 450 / 100; 397 | svg_simple_tag("line",6, 398 | svg_attr("x1", "%d", x), 399 | svg_attr("x2", "%d", x), 400 | svg_attr("y1", "%d", 10), 401 | svg_attr("y2", "%d", y), 402 | svg_attr("stroke", "%s", "black"), 403 | svg_attr("stroke-width", "%f", (i%20 == 10)?1:0.5) 404 | ); 405 | } 406 | 407 | 408 | /*************** Base Ratio ***************/ 409 | 410 | /* Flip svg to make svg coordinate system match cartesian coordinate. Must use 411 | a group since imagemagick uses SVG v1.1*/ 412 | svg_start_tag("g", 1, svg_attr("transform", "translate(%d,%d) scale(%d, %d)", 0, 100, 1,-1)); 413 | 414 | svg_start_tag("svg", 4, 415 | svg_attr("width", "%d", 450), 416 | svg_attr("height", "%d", 100), 417 | svg_attr("preserveAspectRatio", "%s", "none"), 418 | svg_attr("viewBox", "0 0 %d %d", data->max_length, data->number_of_sequences) 419 | ); 420 | 421 | /* Set background color */ 422 | svg_simple_tag("rect", 3, 423 | svg_attr("width", "%s", "100%"), 424 | svg_attr("height", "%s", "100%"), 425 | svg_attr("fill", "%s", "#CCC") 426 | ); 427 | 428 | 429 | /* Allocate 25 characters per base (A,C,T,G) per point. 430 | 4 = max length is capped in kb range, will start compressing if larger 431 | 2 = '.5' added to point 432 | 1 = ',' 433 | 15 = number of reads (10 quadrillion reads will break it) 434 | 1 = ' ' 435 | 2 = padding for miscalculation 436 | 437 | */ 438 | size_t ratio_points_length = 25*data->max_length; 439 | char * ratio_points[4]; 440 | char tmp[25]; 441 | for(i = 0; i < 4; i++){ 442 | ratio_points[i] = malloc(ratio_points_length); 443 | } 444 | 445 | /* Since coordinates for lines and rectangles don't work the same; set the 446 | first point of each line to start off graph. Then, add 0.5 to the x of each 447 | point. Finally, end the line off graph. */ 448 | y = 0; 449 | for(i = 0; i < 4; i++){ 450 | y += data->bases[0].content[i]; 451 | snprintf(ratio_points[i], ratio_points_length, "0,%d ", y); 452 | } 453 | 454 | /* Calculate cumlative sum for each x position and add it to point string */ 455 | for (x = 0; x < data->max_length; x++) { 456 | y = 0; 457 | for(i = 0; i < 4; i++ ){ 458 | y += data->bases[x].content[i]; 459 | 460 | snprintf(tmp, 20, "%d.5,%d ", x, y); 461 | strncat(ratio_points[i], tmp, ratio_points_length); 462 | } 463 | } 464 | 465 | 466 | /* Make lines end off graph */ 467 | y = 0; 468 | for(i = 0; i < 4; i++){ 469 | y += data->bases[data->max_length-1].content[i]; 470 | 471 | snprintf(tmp, 20, "%d,%d ", data->max_length, y); 472 | strncat(ratio_points[i], tmp, ratio_points_length); 473 | } 474 | 475 | 476 | /* Draw each distribution, in decending order so they stack */ 477 | char *ratio_labels[4] = {"%A", "%T", "%C", "%G"}; 478 | char *ratio_colors[4] = {"#648964", "#89bc89", "#84accf", "#5d7992"}; 479 | for(i = 3; i >= 0; i--){ 480 | svg_simple_tag("polyline", 3, 481 | svg_attr("points", "0,0 %s %d,0", ratio_points[i], data->max_length), 482 | svg_attr("fill", "%s", ratio_colors[i]), 483 | svg_attr("stroke", "%s", "none") 484 | ); 485 | } 486 | 487 | for(i = 0; i < 4; i++) 488 | free(ratio_points[i]); 489 | 490 | svg_end_tag("svg"); // Base Ratio 491 | svg_end_tag("g"); // Base Ratio 492 | 493 | /* Lables */ 494 | 495 | svg_start_tag("text", 5, 496 | svg_attr("y", "%d", 95), 497 | svg_attr("fill", "%s", "#CCC"), 498 | svg_attr("x", "%d", 5), 499 | svg_attr("font-family", "%s", "sans-serif"), 500 | svg_attr("font-size", "%s", "15px") 501 | ); 502 | printf("%s\n", "Base Content Percentage"); 503 | svg_end_tag("text"); 504 | 505 | 506 | /* Print Ratio labels in center, only needed the first time 507 | 465 = width of vertical section (450) + width of margin (30) halved 508 | */ 509 | if(position==0){ 510 | for( i = 0; i < 4; i++){ 511 | svg_center_label(465, 20*(4-i), ratio_colors[i], "%s", ratio_labels[i]); 512 | } 513 | } 514 | 515 | if(position == 0){ 516 | svg_axis_label(-50, -5, -90, "Percent"); 517 | svg_axis_number(-5, 100, "end", 0); 518 | svg_axis_number(-5, 5, "end", 100); 519 | }else{ 520 | svg_axis_label(50, -455, 90, "Percent"); 521 | svg_axis_number(455, 100, "start", 0); 522 | svg_axis_number(455, 5, "start", 100); 523 | } 524 | 525 | /*************** Heatmap ***************/ 526 | /* Flip svg to make svg coordinate system match cartesian coordinate. The y 527 | is negative to compensate for the horizontal flip */ 528 | svg_start_tag("g", 1, svg_attr("transform", "translate(%d,%d) scale(%d, %d)", 0, 355, 1,-1)); 529 | 530 | svg_start_tag("svg", 4, 531 | svg_attr("width", "%d", 450), 532 | svg_attr("height", "%d", 250), 533 | svg_attr("preserveAspectRatio", "%s", "none"), 534 | svg_attr("viewBox", "0 0 %d %d", data->max_length, max_score) 535 | ); 536 | 537 | 538 | /* Define background for heatmap. Must be in descending order or highest score 539 | background will overwrite all other backgrounds */ 540 | #define score_back(score, color) \ 541 | svg_simple_tag("rect", 6, \ 542 | svg_attr("x", "%d", 0), \ 543 | svg_attr("y", "%d", 0), \ 544 | svg_attr("width", "%s", "100%"), \ 545 | svg_attr("height", "%d", score), \ 546 | svg_attr("stroke", "%s", "none"), \ 547 | svg_attr("fill", "%s", color) \ 548 | ) 549 | score_back(max_score, "#ccebc5"); // green 550 | score_back(28, "#ffffcc"); // yellow 551 | score_back(20, "#fbb4ae"); // red 552 | 553 | /* Allocate 15 characters per point. 554 | 4 = max length is capped in kb range, will start compressing if larger 555 | 2 = '.5' added to point 556 | 1 = ',' 557 | 5 = '##.##' for float average 558 | 1 = ' ' 559 | 2 = padding for miscalculation 560 | */ 561 | size_t mean_line_points_length = 15*data->max_length; 562 | char * mean_line_points = malloc(mean_line_points_length); 563 | 564 | /* Make line start off graph */ 565 | snprintf(mean_line_points, mean_line_points_length, "0,%0.2f ", averages[0]); 566 | 567 | for (x = 0; x < data->max_length; x++) { 568 | for (y = 0; y < max_score; y++) { 569 | if(data->bases[x].scores[y+offset] > 0) 570 | svg_simple_tag("rect", 8, 571 | svg_attr("x", "%d", x), 572 | svg_attr("y", "%d", y), 573 | svg_attr("fill-opacity", "%f", (float)(data->bases[x].scores[y+offset])/100.0), 574 | svg_attr("width", "%d", 1), 575 | svg_attr("height", "%d", 1), 576 | svg_attr("stroke", "%s", "none"), 577 | svg_attr("stroke-width", "%d", 0), 578 | svg_attr("fill", "%s", "black") 579 | ); 580 | } 581 | 582 | snprintf(tmp, 20, "%d.5,%0.2f ", x, averages[x]); 583 | strncat(mean_line_points, tmp, mean_line_points_length); 584 | } 585 | 586 | /* Make line end off graph */ 587 | snprintf(tmp, 20, "%d,%0.2f", data->max_length, averages[data->max_length-1]); 588 | strncat(mean_line_points, tmp, mean_line_points_length); 589 | 590 | 591 | /* Print mean line */ 592 | svg_simple_tag("polyline", 6, 593 | svg_attr("points", "%s", mean_line_points), 594 | svg_attr("stroke", "%s", "black"), 595 | svg_attr("stroke-width", "%f", 0.5), 596 | svg_attr("stroke-opacity", "%f", 0.5), 597 | svg_attr("fill", "%s", "none"), 598 | svg_attr("stroke-linejoin", "%s", "round") 599 | ); 600 | 601 | free(mean_line_points); 602 | 603 | svg_end_tag("svg"); // Heatmap 604 | svg_end_tag("g"); // Heatmap 605 | 606 | 607 | /* Lables */ 608 | 609 | svg_start_tag("text", 5, 610 | svg_attr("y", "%d", 350), 611 | svg_attr("fill", "%s", "#888"), 612 | svg_attr("x", "%d", 5), 613 | svg_attr("font-family", "%s", "sans-serif"), 614 | svg_attr("font-size", "%s", "15px") 615 | ); 616 | printf("%s\n", "Per Base Sequence Quality"); 617 | svg_end_tag("text"); 618 | 619 | 620 | /* Print base quality labels in center, only needed the first time 621 | 465 = width of vertical section (450) + width of margin (30) halved 622 | 112 = start of graph (105) + half size of text (7) 623 | */ 624 | if(position==0){ 625 | svg_center_label(465, 112, "#888", "%d", max_score); 626 | svg_center_label(465, 112+(int)((max_score-28)*250/max_score), "#888", "%d", 28); 627 | svg_center_label(465, 112+(int)((max_score-20)*250/max_score), "#888", "%d", 20); 628 | } 629 | 630 | 631 | /*************** Length Distro ***************/ 632 | 633 | /* Length Distro graph grows away from heatmap. No need to flip or have 634 | negative y*/ 635 | svg_start_tag("svg", 6, 636 | svg_attr("x", "%d", 0), 637 | svg_attr("y", "%d", 360), 638 | svg_attr("width", "%d", 450), 639 | svg_attr("height", "%d", 100), 640 | svg_attr("preserveAspectRatio", "%s", "none"), 641 | svg_attr("viewBox", "0 0 %d 100", data->max_length) 642 | ); 643 | 644 | /* Set background color */ 645 | svg_simple_tag("rect", 3, 646 | svg_attr("width", "%s", "100%"), 647 | svg_attr("height", "%s", "100%"), 648 | svg_attr("fill", "%s", "#EEE") 649 | ); 650 | 651 | for (x = 0; x < data->max_length; x++) { 652 | if( data->bases[x].length_count > 0) 653 | svg_simple_tag("rect", 6, 654 | svg_attr("x", "%d", x), 655 | svg_attr("y", "%d", 0), 656 | svg_attr("width", "%d", 1), 657 | svg_attr("height", "%d", data->bases[x].length_count), 658 | svg_attr("stroke", "%s", "none"), 659 | svg_attr("fill", "%s", "steelblue") 660 | ); 661 | } 662 | 663 | 664 | 665 | svg_end_tag("svg"); // Length Distro 666 | 667 | 668 | /* Lables */ 669 | 670 | svg_start_tag("text", 5, 671 | svg_attr("y", "%d", 455), 672 | svg_attr("fill", "%s", "#888"), 673 | svg_attr("x", "%d", 5), 674 | svg_attr("font-family", "%s", "sans-serif"), 675 | svg_attr("font-size", "%s", "15px") 676 | ); 677 | printf("%s\n", "Length Distribution"); 678 | svg_end_tag("text"); 679 | 680 | if(position == 0){ 681 | svg_axis_label(-410, -5, -90, "Percent"); 682 | svg_axis_number(-5, 370, "end", 0); 683 | svg_axis_number(-5, 460, "end", 100); 684 | }else{ 685 | svg_axis_label(410, -455, 90, "Percent"); 686 | svg_axis_number(455, 370, "start", 0); 687 | svg_axis_number(455, 460, "start", 100); 688 | } 689 | 690 | 691 | /*************** Adapter Distro ***************/ 692 | 693 | if(adapters_used==1){ 694 | /* Adapter Distro graph grows away from heatmap. No need to flip or have 695 | negative y*/ 696 | svg_start_tag("svg", 6, 697 | svg_attr("x", "%d", 0), 698 | svg_attr("y", "%d", 465), 699 | svg_attr("width", "%d", 450), 700 | svg_attr("height", "%d", 100), 701 | svg_attr("preserveAspectRatio", "%s", "none"), 702 | svg_attr("viewBox", "0 0 %d 100", data->max_length) 703 | ); 704 | 705 | /* Set background color */ 706 | svg_simple_tag("rect", 3, 707 | svg_attr("width", "%s", "100%"), 708 | svg_attr("height", "%s", "100%"), 709 | svg_attr("fill", "%s", "#EEE") 710 | ); 711 | 712 | for (x = 0; x < data->max_length; x++) { 713 | if( data->bases[x].kmer_count > 0) 714 | svg_simple_tag("rect", 6, 715 | svg_attr("x", "%d", x), 716 | svg_attr("y", "%d", 0), 717 | svg_attr("width", "%d", 1), 718 | svg_attr("height", "%d", data->bases[x].kmer_count), 719 | svg_attr("stroke", "%s", "none"), 720 | svg_attr("fill", "%s", "steelblue") 721 | ); 722 | } 723 | 724 | svg_end_tag("svg"); // Adapter Distro 725 | 726 | /* Lables */ 727 | 728 | svg_start_tag("text", 5, 729 | svg_attr("y", "%d", 560), 730 | svg_attr("fill", "%s", "#888"), 731 | svg_attr("x", "%d", 5), 732 | svg_attr("font-family", "%s", "sans-serif"), 733 | svg_attr("font-size", "%s", "15px") 734 | ); 735 | printf("%s\n", "Adapter Distribution"); 736 | svg_end_tag("text"); 737 | 738 | if(position == 0){ 739 | svg_axis_label(-515, -5, -90, "Percent"); 740 | svg_axis_number(-5, 475, "end", 0); 741 | svg_axis_number(-5, 565, "end", 100); 742 | }else{ 743 | svg_axis_label(515, -455, 90, "Percent"); 744 | svg_axis_number(455, 475, "start", 0); 745 | svg_axis_number(455, 565, "start", 100); 746 | } 747 | } 748 | 749 | /*************** Bottom Label ***************/ 750 | y = 470; 751 | if(adapters_used==1) y+=105; 752 | 753 | svg_axis_label(225, y+5, 0, "Base Pairs"); 754 | svg_axis_number(0, y, "middle", 0); 755 | svg_axis_number(450, y, "middle", data->max_length); 756 | 757 | 758 | svg_end_tag("g"); // rug plot vertical section 759 | 760 | /*************** Score Distro ***************/ 761 | 762 | /* Score Distro graph is shown on either side of the heatmap, so it needs to 763 | flip vertically if position == 0. Flipped horizontally as well. Use 764 | negative positions in directions svg is flipped*/ 765 | 766 | svg_start_tag("g", 1, 767 | svg_attr("transform", "translate(%d,%d) scale(%d, %d)", 768 | (position == 0)?125:1065, 355, (position == 0)?-1:1,-1)); 769 | 770 | svg_start_tag("svg", 4, 771 | svg_attr("width", "%d", 100), 772 | svg_attr("height", "%d", 250), 773 | svg_attr("preserveAspectRatio", "%s", "none"), 774 | svg_attr("viewBox", "0 0 100 %d", max_score) 775 | ); 776 | 777 | /* Set background color */ 778 | svg_simple_tag("rect", 3, 779 | svg_attr("width", "%s", "100%"), 780 | svg_attr("height", "%s", "100%"), 781 | svg_attr("fill", "%s", "#EEE") 782 | ); 783 | 784 | for (y = 0; y < max_score; y++) { 785 | if(total_counts[y] > 0) 786 | svg_simple_tag("rect", 6, 787 | svg_attr("x", "%d", 0), 788 | svg_attr("y", "%d", y), 789 | svg_attr("width", "%d", total_counts[y]/number_of_bases), 790 | svg_attr("height", "%d", 1), 791 | svg_attr("stroke", "%s", "none"), 792 | svg_attr("fill", "%s", "steelblue") 793 | ); 794 | } 795 | 796 | svg_end_tag("svg"); // Score Distro 797 | svg_end_tag("g"); // Score Distro 798 | 799 | /* Lables */ 800 | 801 | if(position == 0){ 802 | svg_start_tag("text", 5, 803 | svg_attr("y", "%d", 335), 804 | svg_attr("fill", "%s", "#888"), 805 | svg_attr("x", "%d", 30), 806 | svg_attr("font-family", "%s", "sans-serif"), 807 | svg_attr("font-size", "%s", "15px") 808 | ); 809 | svg_start_tag("tspan", 0); 810 | printf("%s\n", "Score"); 811 | svg_end_tag("tspan"); 812 | 813 | svg_start_tag("tspan", 2, svg_attr("dy", "%d", 15), svg_attr("x", "%d", 30)); 814 | printf("%s\n", "Distribution"); 815 | svg_end_tag("tspan"); 816 | 817 | svg_end_tag("text"); 818 | 819 | svg_axis_label(72, 100, 0, "Percent"); 820 | /* svg_axis_number(125, 100, "middle", 0); */ 821 | svg_axis_number(25, 100, "middle", 100); 822 | 823 | svg_axis_label(-230, 20, -90, "Score"); 824 | svg_axis_number(20, 110, "end", max_score); 825 | svg_axis_number(20, 355, "end", 1); 826 | 827 | }else{ 828 | svg_start_tag("text", 5, 829 | svg_attr("y", "%d", 335), 830 | svg_attr("fill", "%s", "#888"), 831 | svg_attr("x", "%d", 1070), 832 | svg_attr("font-family", "%s", "sans-serif"), 833 | svg_attr("font-size", "%s", "15px") 834 | ); 835 | svg_start_tag("tspan", 0); 836 | printf("%s\n", "Score"); 837 | svg_end_tag("tspan"); 838 | 839 | svg_start_tag("tspan", 2, svg_attr("dy", "%d", 15), svg_attr("x", "%d", 1070)); 840 | printf("%s\n", "Distribution"); 841 | svg_end_tag("tspan"); 842 | 843 | svg_end_tag("text"); 844 | 845 | svg_axis_label(1115, 100, 0, "Percent"); 846 | /* svg_axis_number(1070, 100, "middle", 0); */ 847 | svg_axis_number(1165, 100, "middle", 100); 848 | 849 | svg_axis_label(230, -1170, 90, "Score"); 850 | svg_axis_number(1170, 110, "start", max_score); 851 | svg_axis_number(1170, 355, "start", 1); 852 | } 853 | 854 | svg_end_tag("g"); // rug plot 855 | 856 | } 857 | 858 | int main (int argc, char **argv) 859 | { 860 | struct arguments arguments; 861 | arguments = parse_options(argc, argv); 862 | 863 | int paired, unpaired, adapters; 864 | int width, height; 865 | int *kmers = NULL; 866 | 867 | paired = (arguments.forward != NULL && arguments.reverse != NULL); 868 | unpaired = (arguments.unpaired != NULL); 869 | adapters = (arguments.adapters != NULL); 870 | 871 | /* If paired and unparied data are both set or unset, then throw error */ 872 | if(paired == unpaired){ 873 | printf("%s\n", "Usage: quack [OPTION...]\nTry `quack --help' or `quack --usage' for more information."); 874 | exit(1); 875 | } 876 | 877 | if(adapters) kmers = read_adapters(arguments.adapters); 878 | 879 | width = (paired)?1195:615; 880 | height = (adapters)?610:510; 881 | 882 | if(arguments.name != NULL) 883 | height += 30; 884 | 885 | svg_start_tag("svg", 5, 886 | svg_attr("width", "%d", width), 887 | svg_attr("height", "%d", height), 888 | svg_attr("viewBox", "%d %d %d %d", 0, 0, width, height), 889 | svg_attr("xmlns", "%s", "http://www.w3.org/2000/svg"), 890 | svg_attr("xmlns:xlink", "%s", "http://www.w3.org/1999/xlink") 891 | ); 892 | 893 | // If name is given, add to middle of viewBox (half of width + min-x of viewbox) 894 | if(arguments.name != NULL){ 895 | svg_start_tag("text", 6, 896 | svg_attr("x", "%d", (width/2)), 897 | svg_attr("y", "%d", 30), 898 | svg_attr("font-family", "%s", "sans-serif"), 899 | svg_attr("text-anchor", "%s", "middle"), 900 | svg_attr("font-size", "%s", "30px"), 901 | svg_attr("fill", "%s", "black")); 902 | printf("%s", arguments.name); 903 | svg_end_tag("text"); 904 | 905 | svg_start_tag("g", 1, 906 | svg_attr("transform", "translate(%d %d)", 0, 30) 907 | ); 908 | 909 | } 910 | 911 | sequence_data *data = read_fastq(((paired)?arguments.forward:arguments.unpaired), kmers); 912 | sequence_data *transformed_data = transform(data); 913 | draw(transformed_data, 0, adapters); 914 | free(data); 915 | 916 | if(paired){ 917 | data = read_fastq(arguments.reverse, kmers); 918 | transformed_data = transform(data); 919 | draw(transformed_data, 1, adapters); 920 | free(data); 921 | } 922 | 923 | if(arguments.name != NULL) svg_end_tag("g"); 924 | 925 | svg_end_tag("svg"); 926 | 927 | exit (0); 928 | } 929 | -------------------------------------------------------------------------------- /svg.c: -------------------------------------------------------------------------------- 1 | #include "svg.h" 2 | 3 | #include 4 | #include 5 | #include 6 | #include 7 | 8 | #define INDENT " " 9 | int _svg_indent_level = 0; 10 | 11 | 12 | char* svg_attr(const char* name, const char* fmt, ...){ 13 | char *attr; 14 | int retval, length, cur_length; 15 | va_list vl; 16 | 17 | /* Use vsnprintf to get the length of value string before allocating memory*/ 18 | va_start(vl, fmt); 19 | retval = vsnprintf(NULL, 0, fmt, vl); 20 | va_end(vl); 21 | if(retval < 0) return NULL; 22 | 23 | /* Allocate enough memory for entire attribute string: 24 | ' $name="$value"' 25 | length($name) + length($value) + 4 literals [ =""] + null char 26 | */ 27 | length = retval + strlen(name) + 5; 28 | attr = malloc(length); 29 | if(attr == NULL) return NULL; 30 | 31 | 32 | /* Print beginning of attribute: ' $name="' ; freeing memory if failed*/ 33 | retval = snprintf(attr, length-1, " %s=\"", name); 34 | if(retval < 0){ 35 | free(attr); 36 | return NULL; 37 | } 38 | cur_length = retval; 39 | 40 | /* Print attribute value; freeing memory if failed*/ 41 | va_start(vl, fmt); 42 | retval = vsnprintf(attr + cur_length, length-cur_length-1, fmt, vl); 43 | va_end(vl); 44 | if(retval < 0){ 45 | free(attr); 46 | return NULL; 47 | } 48 | cur_length += retval; 49 | 50 | /* Close quote and terminate string */ 51 | attr[cur_length] = '"'; 52 | attr[cur_length+1] = '\0'; 53 | 54 | return attr; 55 | } 56 | 57 | 58 | 59 | void _svg_tag(const int simple, const char* type, int num, ...){ 60 | int i = 0; 61 | va_list vl; 62 | char* attr; 63 | 64 | /* Indent current tag */ 65 | for( i = 0; i < _svg_indent_level; i++) 66 | printf(INDENT); 67 | 68 | /* Increase indent level if started tag with internal elements */ 69 | if(!simple) 70 | _svg_indent_level++; 71 | 72 | /* Open tag */ 73 | printf("<%s", type); 74 | 75 | /* Print each attribute, free memory as used */ 76 | va_start(vl, num); 77 | for(i = 0; i < num; i++){ 78 | attr = va_arg(vl, char*); 79 | printf("%s", attr); 80 | free(attr); 81 | } 82 | va_end(vl); 83 | 84 | /* print nested closing tag if no internal elements expected */ 85 | if(simple) printf("/"); 86 | 87 | /* close tag */ 88 | printf(">\n"); 89 | } 90 | 91 | 92 | void svg_end_tag(const char* type){ 93 | int i = 0; 94 | 95 | if(_svg_indent_level > 0) 96 | _svg_indent_level--; 97 | 98 | for( i = 0; i < _svg_indent_level; i++) 99 | printf(INDENT); 100 | 101 | 102 | printf("\n", type); 103 | 104 | } 105 | -------------------------------------------------------------------------------- /svg.h: -------------------------------------------------------------------------------- 1 | #ifndef __SVG_H 2 | #define __SVG_H 3 | 4 | /* Add an attribute to the svg tag. 5 | - `name` = name of attribute. 6 | - `fmt` = printf format 7 | - `...` = are variables passed to printf 8 | */ 9 | /* #define svg_attr(name, type, ...) " " #name "=" #type , __VA_ARGS__ */ 10 | char* svg_attr(const char* name, const char* fmt, ...); 11 | 12 | /* Print an svg tag (i.e ). `svg_start_tag` doesn't add a final '/', 13 | while `svg_simple_tag` does. 14 | - `type` = type of element (e.g. 'svg', 'line', 'rect', etc) 15 | - `num` = number of attributes 16 | - `...` = a list of svg_attr 17 | */ 18 | void _svg_tag(const int simple, const char* type, int num, ...); 19 | #define svg_start_tag(...) _svg_tag(0, __VA_ARGS__) 20 | #define svg_simple_tag(...) _svg_tag(1, __VA_ARGS__) 21 | 22 | 23 | /* Prints closing svg tag (i.e ). 24 | - `type` = type of element (e.g. 'svg', 'line', 'rect', etc) 25 | */ 26 | void svg_end_tag(const char* type); 27 | 28 | 29 | #endif 30 | --------------------------------------------------------------------------------