├── .gitignore ├── .travis.yml ├── COPYING ├── Changelog ├── Makefile ├── README.md ├── redist ├── Makefile ├── boost_1_44_0_subset.tar.bz2 └── tabix_v0.2.6_with_faidx.tar.gz ├── scratch ├── code_header_scripts │ ├── new_header │ ├── reheader.pl │ └── runit.bash ├── make_boost_subset.bash ├── make_release_tarball.bash ├── run_astyle.bash └── todo.triotwins ├── src ├── Makefile ├── break_blocks.cpp ├── check_reference.cpp ├── extract_variants.cpp ├── gatk_to_gvcf.cpp ├── getBamAvgChromDepth.pl ├── get_called_regions.cpp ├── gvcftools.hh.in ├── libblock │ ├── BlockVcfRecord.cpp │ ├── BlockVcfRecord.hh │ ├── BlockerOptions.cpp │ ├── BlockerOptions.hh │ ├── BlockerStats.cpp │ ├── BlockerStats.hh │ ├── BlockerVcfHeaderHandler.cpp │ ├── BlockerVcfHeaderHandler.hh │ ├── GatkVcfRecord.cpp │ ├── GatkVcfRecord.hh │ ├── Makefile │ ├── RegionVcfRecordHandler.cpp │ ├── RegionVcfRecordHandler.hh │ ├── VcfHeaderHandler.cpp │ ├── VcfHeaderHandler.hh │ ├── VcfRecord.cpp │ ├── VcfRecord.hh │ ├── VcfRecordBlocker.cpp │ └── VcfRecordBlocker.hh ├── libtrio │ ├── Makefile │ ├── gzlinereader.cpp │ ├── gzlinereader.hh │ ├── related_sample_util.cpp │ ├── related_sample_util.hh │ ├── tabix_streamer.cpp │ ├── tabix_streamer.hh │ ├── tabix_util.cpp │ ├── tabix_util.hh │ ├── trio_option_util.cpp │ └── trio_option_util.hh ├── libutil │ ├── Makefile │ ├── blt_exception.cpp │ ├── blt_exception.hh │ ├── compat_util.cpp │ ├── compat_util.hh │ ├── id_map.hh │ ├── istream_line_splitter.cpp │ ├── istream_line_splitter.hh │ ├── parse_util.cpp │ ├── parse_util.hh │ ├── pos_type.hh │ ├── print_double.cpp │ ├── print_double.hh │ ├── ref_util.cpp │ ├── ref_util.hh │ ├── reference_contig_segment.hh │ ├── region_util.cpp │ ├── region_util.hh │ ├── scan_string.hh │ ├── seq_util.cpp │ ├── seq_util.hh │ ├── stream_stat.cpp │ ├── stream_stat.hh │ ├── string_util.cpp │ ├── string_util.hh │ ├── stringer.cpp │ ├── stringer.hh │ ├── test │ │ ├── compat_util_test.cpp │ │ ├── istream_line_splitter_test.cpp │ │ ├── parse_util_test.cpp │ │ ├── stringutil_test.cpp │ │ └── test_main.cpp │ ├── vcf_util.cpp │ └── vcf_util.hh ├── merge_variants.cpp ├── remove_region.cpp ├── set_haploid_region.cpp ├── trio.cpp └── twins.cpp └── test ├── blocktest1 └── data │ └── gatk_allsites.vcf.gz ├── notes ├── triotest1 ├── data │ ├── NA19238.chr6:57481680-57481745.vcf.gz │ ├── NA19239.chr6:57481680-57481745.vcf.gz │ └── NA19240.chr6:57481680-57481745.vcf.gz └── notes └── twintest1 ├── data ├── twin1.vcf.gz ├── twin1.vcf.gz.tbi ├── twin2.vcf.gz └── twin2.vcf.gz.tbi ├── expected_output.txt ├── notes └── runit.bash /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/.travis.yml -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/COPYING -------------------------------------------------------------------------------- /Changelog: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/Changelog -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/README.md -------------------------------------------------------------------------------- /redist/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/redist/Makefile -------------------------------------------------------------------------------- /redist/boost_1_44_0_subset.tar.bz2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/redist/boost_1_44_0_subset.tar.bz2 -------------------------------------------------------------------------------- /redist/tabix_v0.2.6_with_faidx.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/redist/tabix_v0.2.6_with_faidx.tar.gz -------------------------------------------------------------------------------- /scratch/code_header_scripts/new_header: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/code_header_scripts/new_header -------------------------------------------------------------------------------- /scratch/code_header_scripts/reheader.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/code_header_scripts/reheader.pl -------------------------------------------------------------------------------- /scratch/code_header_scripts/runit.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/code_header_scripts/runit.bash -------------------------------------------------------------------------------- /scratch/make_boost_subset.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/make_boost_subset.bash -------------------------------------------------------------------------------- /scratch/make_release_tarball.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/make_release_tarball.bash -------------------------------------------------------------------------------- /scratch/run_astyle.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/run_astyle.bash -------------------------------------------------------------------------------- /scratch/todo.triotwins: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/scratch/todo.triotwins -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/Makefile -------------------------------------------------------------------------------- /src/break_blocks.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/break_blocks.cpp -------------------------------------------------------------------------------- /src/check_reference.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/check_reference.cpp -------------------------------------------------------------------------------- /src/extract_variants.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/extract_variants.cpp -------------------------------------------------------------------------------- /src/gatk_to_gvcf.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/gatk_to_gvcf.cpp -------------------------------------------------------------------------------- /src/getBamAvgChromDepth.pl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/getBamAvgChromDepth.pl -------------------------------------------------------------------------------- /src/get_called_regions.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/get_called_regions.cpp -------------------------------------------------------------------------------- /src/gvcftools.hh.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/gvcftools.hh.in -------------------------------------------------------------------------------- /src/libblock/BlockVcfRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockVcfRecord.cpp -------------------------------------------------------------------------------- /src/libblock/BlockVcfRecord.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockVcfRecord.hh -------------------------------------------------------------------------------- /src/libblock/BlockerOptions.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockerOptions.cpp -------------------------------------------------------------------------------- /src/libblock/BlockerOptions.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockerOptions.hh -------------------------------------------------------------------------------- /src/libblock/BlockerStats.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockerStats.cpp -------------------------------------------------------------------------------- /src/libblock/BlockerStats.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockerStats.hh -------------------------------------------------------------------------------- /src/libblock/BlockerVcfHeaderHandler.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockerVcfHeaderHandler.cpp -------------------------------------------------------------------------------- /src/libblock/BlockerVcfHeaderHandler.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/BlockerVcfHeaderHandler.hh -------------------------------------------------------------------------------- /src/libblock/GatkVcfRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/GatkVcfRecord.cpp -------------------------------------------------------------------------------- /src/libblock/GatkVcfRecord.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/GatkVcfRecord.hh -------------------------------------------------------------------------------- /src/libblock/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/Makefile -------------------------------------------------------------------------------- /src/libblock/RegionVcfRecordHandler.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/RegionVcfRecordHandler.cpp -------------------------------------------------------------------------------- /src/libblock/RegionVcfRecordHandler.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/RegionVcfRecordHandler.hh -------------------------------------------------------------------------------- /src/libblock/VcfHeaderHandler.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/VcfHeaderHandler.cpp -------------------------------------------------------------------------------- /src/libblock/VcfHeaderHandler.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/VcfHeaderHandler.hh -------------------------------------------------------------------------------- /src/libblock/VcfRecord.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/VcfRecord.cpp -------------------------------------------------------------------------------- /src/libblock/VcfRecord.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/VcfRecord.hh -------------------------------------------------------------------------------- /src/libblock/VcfRecordBlocker.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/VcfRecordBlocker.cpp -------------------------------------------------------------------------------- /src/libblock/VcfRecordBlocker.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libblock/VcfRecordBlocker.hh -------------------------------------------------------------------------------- /src/libtrio/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/Makefile -------------------------------------------------------------------------------- /src/libtrio/gzlinereader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/gzlinereader.cpp -------------------------------------------------------------------------------- /src/libtrio/gzlinereader.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/gzlinereader.hh -------------------------------------------------------------------------------- /src/libtrio/related_sample_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/related_sample_util.cpp -------------------------------------------------------------------------------- /src/libtrio/related_sample_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/related_sample_util.hh -------------------------------------------------------------------------------- /src/libtrio/tabix_streamer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/tabix_streamer.cpp -------------------------------------------------------------------------------- /src/libtrio/tabix_streamer.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/tabix_streamer.hh -------------------------------------------------------------------------------- /src/libtrio/tabix_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/tabix_util.cpp -------------------------------------------------------------------------------- /src/libtrio/tabix_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/tabix_util.hh -------------------------------------------------------------------------------- /src/libtrio/trio_option_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/trio_option_util.cpp -------------------------------------------------------------------------------- /src/libtrio/trio_option_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libtrio/trio_option_util.hh -------------------------------------------------------------------------------- /src/libutil/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/Makefile -------------------------------------------------------------------------------- /src/libutil/blt_exception.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/blt_exception.cpp -------------------------------------------------------------------------------- /src/libutil/blt_exception.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/blt_exception.hh -------------------------------------------------------------------------------- /src/libutil/compat_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/compat_util.cpp -------------------------------------------------------------------------------- /src/libutil/compat_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/compat_util.hh -------------------------------------------------------------------------------- /src/libutil/id_map.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/id_map.hh -------------------------------------------------------------------------------- /src/libutil/istream_line_splitter.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/istream_line_splitter.cpp -------------------------------------------------------------------------------- /src/libutil/istream_line_splitter.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/istream_line_splitter.hh -------------------------------------------------------------------------------- /src/libutil/parse_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/parse_util.cpp -------------------------------------------------------------------------------- /src/libutil/parse_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/parse_util.hh -------------------------------------------------------------------------------- /src/libutil/pos_type.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/pos_type.hh -------------------------------------------------------------------------------- /src/libutil/print_double.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/print_double.cpp -------------------------------------------------------------------------------- /src/libutil/print_double.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/print_double.hh -------------------------------------------------------------------------------- /src/libutil/ref_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/ref_util.cpp -------------------------------------------------------------------------------- /src/libutil/ref_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/ref_util.hh -------------------------------------------------------------------------------- /src/libutil/reference_contig_segment.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/reference_contig_segment.hh -------------------------------------------------------------------------------- /src/libutil/region_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/region_util.cpp -------------------------------------------------------------------------------- /src/libutil/region_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/region_util.hh -------------------------------------------------------------------------------- /src/libutil/scan_string.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/scan_string.hh -------------------------------------------------------------------------------- /src/libutil/seq_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/seq_util.cpp -------------------------------------------------------------------------------- /src/libutil/seq_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/seq_util.hh -------------------------------------------------------------------------------- /src/libutil/stream_stat.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/stream_stat.cpp -------------------------------------------------------------------------------- /src/libutil/stream_stat.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/stream_stat.hh -------------------------------------------------------------------------------- /src/libutil/string_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/string_util.cpp -------------------------------------------------------------------------------- /src/libutil/string_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/string_util.hh -------------------------------------------------------------------------------- /src/libutil/stringer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/stringer.cpp -------------------------------------------------------------------------------- /src/libutil/stringer.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/stringer.hh -------------------------------------------------------------------------------- /src/libutil/test/compat_util_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/test/compat_util_test.cpp -------------------------------------------------------------------------------- /src/libutil/test/istream_line_splitter_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/test/istream_line_splitter_test.cpp -------------------------------------------------------------------------------- /src/libutil/test/parse_util_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/test/parse_util_test.cpp -------------------------------------------------------------------------------- /src/libutil/test/stringutil_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/test/stringutil_test.cpp -------------------------------------------------------------------------------- /src/libutil/test/test_main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/test/test_main.cpp -------------------------------------------------------------------------------- /src/libutil/vcf_util.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/vcf_util.cpp -------------------------------------------------------------------------------- /src/libutil/vcf_util.hh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/libutil/vcf_util.hh -------------------------------------------------------------------------------- /src/merge_variants.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/merge_variants.cpp -------------------------------------------------------------------------------- /src/remove_region.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/remove_region.cpp -------------------------------------------------------------------------------- /src/set_haploid_region.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/set_haploid_region.cpp -------------------------------------------------------------------------------- /src/trio.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/trio.cpp -------------------------------------------------------------------------------- /src/twins.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/src/twins.cpp -------------------------------------------------------------------------------- /test/blocktest1/data/gatk_allsites.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/blocktest1/data/gatk_allsites.vcf.gz -------------------------------------------------------------------------------- /test/notes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/notes -------------------------------------------------------------------------------- /test/triotest1/data/NA19238.chr6:57481680-57481745.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/triotest1/data/NA19238.chr6:57481680-57481745.vcf.gz -------------------------------------------------------------------------------- /test/triotest1/data/NA19239.chr6:57481680-57481745.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/triotest1/data/NA19239.chr6:57481680-57481745.vcf.gz -------------------------------------------------------------------------------- /test/triotest1/data/NA19240.chr6:57481680-57481745.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/triotest1/data/NA19240.chr6:57481680-57481745.vcf.gz -------------------------------------------------------------------------------- /test/triotest1/notes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/triotest1/notes -------------------------------------------------------------------------------- /test/twintest1/data/twin1.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/data/twin1.vcf.gz -------------------------------------------------------------------------------- /test/twintest1/data/twin1.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/data/twin1.vcf.gz.tbi -------------------------------------------------------------------------------- /test/twintest1/data/twin2.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/data/twin2.vcf.gz -------------------------------------------------------------------------------- /test/twintest1/data/twin2.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/data/twin2.vcf.gz.tbi -------------------------------------------------------------------------------- /test/twintest1/expected_output.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/expected_output.txt -------------------------------------------------------------------------------- /test/twintest1/notes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/notes -------------------------------------------------------------------------------- /test/twintest1/runit.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sequencing/gvcftools/HEAD/test/twintest1/runit.bash --------------------------------------------------------------------------------