├── ContigsCompactor-v0.2.0 └── ContigsMerger │ ├── ._ContigsCompactor.cpp │ ├── ._ContigsCompactor.h │ ├── ._GenSeqsUtils.cpp │ ├── ._GenSeqsUtils.h │ ├── ._GraphUtils.cpp │ ├── ._GraphUtils.h │ ├── ._KmerUtils.cpp │ ├── ._KmerUtils.h │ ├── ._Utils-basic.cpp │ ├── ._Utils-basic.h │ ├── ._abstractcharsequence.cpp │ ├── ._abstractcharsequence.h │ ├── ._fastaMultiSeqs.cpp │ ├── ._fastaMultiSeqs.h │ ├── ._fastareader.cpp │ ├── ._fastareader.h │ ├── ._main.cpp │ ├── .vs │ └── ContigsMerger │ │ └── v14 │ │ └── .suo │ ├── ContigsCompactor.cpp │ ├── ContigsCompactor.cpp.bak │ ├── ContigsCompactor.h │ ├── ContigsCompactor1.cpp │ ├── ContigsMerger │ ├── ContigsMerger.sdf │ ├── ContigsMerger.sln │ ├── ContigsMerger.vcxproj │ ├── ContigsMerger.vcxproj.filters │ ├── GenSeqsUtils.cpp │ ├── GenSeqsUtils.h │ ├── GraphUtils.cpp │ ├── GraphUtils.h │ ├── KmerUtils.cpp │ ├── KmerUtils.cpp.bak │ ├── KmerUtils.h │ ├── Makefile │ ├── MurmurHash3.cpp │ ├── MurmurHash3.h │ ├── ScaffoldUtils.cpp │ ├── ScaffoldUtils.h │ ├── Utils-basic.cpp │ ├── Utils-basic.h │ ├── abstractcharsequence.cpp │ ├── abstractcharsequence.h │ ├── checkDiff.py │ ├── fastaMultiSeqs.cpp │ ├── fastaMultiSeqs.h │ ├── fastareader.cpp │ ├── fastareader.h │ ├── main.cpp │ ├── merged.sort.bam │ ├── merged.sort.bam.bai │ └── parseQualifiedContigsFromBlast.py ├── ContigsMerger ├── MergeContigs.py ├── README.md ├── TERefiner ├── .vs │ └── TERefiner │ │ └── v14 │ │ └── .suo ├── Alignment.cpp ├── Alignment.h ├── Coverage.cpp ├── Coverage.h ├── HardClipReads.cpp ├── HardClipReads.h ├── Makefile ├── RepeatsClassifier.cpp ├── RepeatsClassifier.h ├── StrOperation.cpp ├── StrOperation.h ├── TERefiner.sdf ├── TERefiner.sln ├── TERefiner.vcxproj ├── TERefiner.vcxproj.filters ├── TERefiner.vcxproj.user ├── TERefiner_1 ├── algorithms │ ├── local_alignment.cpp │ ├── local_alignment.h │ ├── smith-waterman.cpp │ ├── smith-waterman.h │ └── stdaln.h ├── bam_alignment_record.h ├── bam_header_record.h ├── bam_parse.cpp ├── bam_parse.h ├── contigs.cpp ├── contigs.h ├── fai_parser.cpp ├── fai_parser.h ├── fasta_parser.cpp ├── fasta_parser.h ├── insert_size.cpp ├── insert_size.h ├── khash.h ├── kseq.h ├── main.cpp ├── public_func.cpp ├── public_func.h ├── public_parameters.h ├── refiner.cpp ├── refiner.h ├── scaffolding.cpp ├── scaffolding.h └── test_code │ ├── HG01890_keep_used.sort.bam │ ├── HG01890_keep_used.sort.bam.bai │ ├── HG01890_remove_used_has_upper_bound_keep_all_20_0.2.fa.no_dup.fa.merged.fa.sort.bam │ ├── HG01890_remove_used_has_upper_bound_keep_all_20_0.2.fa.no_dup.fa.merged.fa.sort.bam.bai │ ├── humrep.ref │ └── humrep.ref.fai ├── TERefiner_1 ├── Utility.py ├── assemble_gaps.py ├── clear_temp.py ├── collect_both_unmapped_reads.py ├── collect_discordant_low_mapq_reads.py ├── collect_reads_for_gaps.py ├── configuration.json ├── discordant_alignment_statistic.py ├── get_filled_seq_from_out_scf.py ├── gnrt_pos_true_seqs.py ├── main.py ├── merge_reads.py ├── pick_contigs.py ├── put_gap_seq_back_to_scaffold.py 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