├── .gitattributes ├── .gitignore ├── LICENSE ├── README.md ├── breakpoint2vcf └── breakpoint2vcf.py ├── example ├── bin │ ├── bwa │ ├── samtools │ └── seeksv ├── cancer.somatic.sv ├── cancer.sort.bam ├── cancer.sort.bam.bai ├── cancer.sv ├── normal.sort.bam ├── normal.sort.bam.bai ├── normal.sv ├── reference │ ├── example.fa │ ├── example.fa.amb │ ├── example.fa.ann │ ├── example.fa.bwt │ ├── example.fa.fai │ ├── example.fa.pac │ └── example.fa.sa ├── seeksv.sh ├── seeksv.somatic.sh └── simu_data │ ├── cancer.del.info │ └── normal.del.info ├── sam ├── bam.h ├── bgzf.h ├── faidx.h ├── glf.h ├── khash.h ├── knetfile.h ├── kstring.h ├── libbam.a ├── razf.h ├── sam.h ├── sam_header.h ├── sam_view.h ├── xcurses.h ├── zconf.h └── zlib.h ├── seeksv ├── Makefile ├── README ├── bam2depth.cpp ├── bam2depth.h ├── clip_reads.cpp ├── clip_reads.h ├── cluster.cpp ├── cluster.h ├── getsv.cpp ├── getsv.h ├── gzstream.C ├── gzstream.h ├── head.h ├── main.cpp ├── process_bwasw.cpp ├── process_bwasw.h ├── seeksv ├── seeksv.cpp ├── somatic.cpp └── somatic.h └── svcompare ├── Makefile ├── junction.h ├── svcompare ├── svcompare.cpp └── update.log /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qiukunlong/seeksv/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qiukunlong/seeksv/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/qiukunlong/seeksv/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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