├── .gitignore ├── .gitmodules ├── LICENSE ├── Makefile ├── README.md ├── algorithm ├── align │ ├── AlignReuslt.h │ ├── NeedlemanWunsch.h │ ├── ScoreMatrix.h │ ├── ScoreSchemes.h │ ├── SmithWaterman.h │ └── SmithWaterman_test.cpp ├── bi_list │ ├── bi_list.h │ └── bi_list_test.cpp ├── collection │ ├── collection.h │ └── collection_test.cpp ├── disjoin_set │ ├── disjoin_set.cpp │ └── disjoin_set.h ├── distribution │ ├── distribution.h │ └── distribution_test.cpp ├── fibheap │ ├── fib_heap.h │ └── fib_heap_test.cpp ├── graph │ ├── DepthSearch.h │ ├── Graph.h │ ├── GraphBasic.h │ ├── GraphBasic_test.cpp │ ├── GraphTest.cpp │ ├── GraphTipRemove.h │ ├── GraphTipRemove_test.cpp │ ├── GraphTrunk.h │ ├── GraphTrunk_test.cpp │ ├── MinTree.h │ ├── MinTree_test.cpp │ ├── SPFSearch.h │ └── SPFSearch_test.cpp ├── incr_array │ ├── incr_array.h │ └── incr_array_test.cpp ├── interval │ ├── Interval.h │ └── Interval_test.cpp ├── linear_fitting │ ├── Linear.h │ ├── Minimum_multiplication.h │ └── Minimum_multiplication_test.cpp ├── multi_key_hash │ └── MultiKeyHash.h └── statistics │ └── common.h ├── appcommon ├── AlignMinimap2.h ├── NonRepeatFilter.h ├── NonRepeatFilter_test.cpp ├── ONT2Gap.cpp ├── ONT2Gap.h ├── ScaffInfo.cpp ├── ScaffInfo.h ├── SmithWaterman_OO.h ├── SubSets.h ├── SubSets_test.cpp ├── contigPairInfo.cpp ├── contigPairInfo.h └── fileName.h ├── biocommon ├── align_common │ ├── align_result.cpp │ └── align_result.h ├── fasta │ ├── fasta.cpp │ ├── fasta.h │ └── fasta_test.cpp ├── fastq │ ├── fastq.cpp │ ├── fastq.h │ └── fastq_test.cpp ├── paf │ ├── PAF.cpp │ └── PAF.h ├── pair │ ├── pair_sam_parser.cpp │ └── pair_sam_parser.h ├── sam_bam │ ├── .gitignore │ ├── sam_parser.cpp │ ├── sam_parser.h │ └── sam_parser_test.cpp └── seq │ ├── seq.cpp │ ├── seq.h │ ├── seq_test.cpp │ └── tool_func.h ├── common ├── args │ ├── argsparser.cpp │ ├── argsparser.h │ └── argsparser_test.cpp ├── error │ └── Error.h ├── files │ ├── .gitignore │ ├── file_reader.cpp │ ├── file_reader.h │ ├── file_test.cpp │ ├── file_writer.cpp │ ├── file_writer.h │ ├── gzstream.cpp │ └── gzstream.h ├── flags │ └── flags.h ├── freq │ └── freq.h ├── log │ ├── log.cpp │ ├── log.h │ ├── logfilter.cpp │ └── logfilter.h ├── middle_valiad │ └── MiddleValid.h ├── multithread │ ├── Job.h │ ├── JobQueue.h │ └── MultiThread.h ├── stl │ └── mapHelper.h ├── string │ ├── stringtools.cpp │ ├── stringtools.h │ └── stringtools_test.cpp ├── test │ ├── Check.h │ └── Test.h └── time │ ├── timetools.cpp │ ├── timetools.h │ └── timetools_test.cpp ├── discards ├── DiffONTPilon.cpp ├── ONTGapCorrecter.cpp ├── ONTGapDev01.cpp ├── ORGC.cpp ├── SplitScaff2NamedContig.cpp ├── TGSFiller_pipeline.sh ├── TGSFiller_pipelineP.sh ├── TGSFiller_racon.sh ├── filter_gap_filler.sh ├── gen_subont.awk ├── samSQ_filter.awk ├── samSQ_filter.c └── samSQ_filter.cpp ├── example ├── README.md ├── input.scaff.fasta ├── ngs.reads.fastq └── ont.reads.fasta ├── main_src_ont ├── GenMake.sh ├── Makefile ├── tgsgapcandidate.cpp ├── tgsgapcloser.cpp ├── tgsseqgen.cpp └── tgsseqsplit.cpp ├── main_src_tool ├── Contig100K.cpp ├── ExtractFakeFill.cpp ├── ExtractRealFill.awk ├── FakeRef2Scaff.cpp ├── GenMake.sh ├── Makefile └── Ref2Gap.cpp ├── orientation_correct ├── Makefile ├── ONT_OrientationCorrecter.cpp ├── ONT_OrientationCorrecterV1.cpp ├── ONT_OrientationCorrecterV2.cpp ├── ONT_OrientationCorrecterV3.cpp ├── ONT_contigmapper.cpp ├── OOChecker.cpp ├── Quast2OO.cpp ├── README.md ├── ScaffInfo.cpp ├── ScaffInfo.h ├── TriContigDetect.cpp ├── contigPairInfo.cpp ├── contigPairInfo.h ├── filter_oo.py └── pipeline.sh ├── test ├── Makefile └── test.cpp └── tgsgapcloser /.gitignore: -------------------------------------------------------------------------------- 1 | *.o 2 | bin 3 | tool 4 | tags 5 | .ycm_extra_conf.py 6 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 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