├── .github ├── actions │ ├── build-test │ │ └── action.yml │ └── setup-htslib │ │ └── action.yml └── workflows │ ├── cmake_htslib.yml │ ├── integration-test.yml │ └── workflow-test.yml ├── .gitignore ├── CMakeLists.txt ├── CMakeLists.txt.in ├── INSTALL.md ├── LICENSE ├── README.md ├── configs ├── bowtie2.yaml ├── default.yaml ├── ont.yaml ├── ont_all.yaml ├── pacbio.yaml └── pacbio_all.yaml ├── docker ├── env │ └── Dockerfile ├── production │ └── Dockerfile └── update_docker.sh ├── figures ├── levioSAM_S_bw.png └── levioSAM_S_bw_dark.png ├── invert.py ├── leviosam-test.py ├── scripts ├── chain_invert.py ├── chain_utils.py ├── collect_perf.py ├── compare_fastq.py ├── compare_sam-test.py ├── compare_sam.py ├── extract_seq_from_bed.py ├── extract_unpaired_reads.py ├── fai_to_bed.py ├── filter_bed_by_size.py ├── gen_length_map.py ├── get_low_identity_regions.py ├── get_mappable_regions.py ├── leviosam_utils-test.py ├── leviosam_utils.py ├── mask_fasta_with_bed.py ├── sam_qname_to_bed.py ├── sample_fq.py ├── summarize_aln_features.py ├── testdata │ ├── chr1_1_100000.fa │ ├── chr1_1_100000.fa.fai │ ├── chr1_test1.bed │ ├── mask_fasta_with_bed-chr1_test1.fa.results │ └── mask_fasta_with_bed-chr1_test1.fa.results.fai ├── vcf2chain.sh ├── vcf_to_bed.sh └── verbosify_chain.py ├── src ├── IITree.h ├── aln.cpp ├── aln.hpp ├── bam.h ├── bam_aux.c ├── bam_md.c ├── bed.cpp ├── bed.hpp ├── bed_test.cpp ├── chain.cpp ├── chain.hpp ├── chain_test.cpp ├── cigar.cpp ├── cigar.hpp ├── cigar_test.cpp ├── collate.cpp ├── collate.hpp ├── gzstream.C ├── gzstream.h ├── ksw2.h ├── ksw2_extd2_sse.c ├── ksw2_extz.c ├── ksw2_extz2_sse.c ├── leviosam.cpp ├── leviosam.hpp ├── leviosam_utils.cpp ├── leviosam_utils.hpp ├── leviosam_utils_test.cpp ├── lift_bed.cpp ├── lift_bed.hpp ├── rapidyaml.hpp ├── reconcile.cpp ├── reconcile.hpp ├── reconcile_test.cpp ├── robin_hood.h ├── sse2neon │ └── sse2neon.h ├── version.hpp ├── yaml.cpp └── yaml.hpp ├── testdata ├── HG002-0.3x-bwa-grch37-chr1_rev.sam ├── HG002-0.3x-bwa-grch38-chr1_rev.sam ├── bt2-pe-chm13_v1.1_hg2y.bam ├── bt2-pe-grch38.bam ├── bt2-pe-major.bam ├── bt2-se-chm13_v1.1_hg2y.bam ├── bt2-se-grch38.bam ├── bt2-se-major.bam ├── bwa-pe-chm13_v1.1_hg2y.bam ├── bwa-pe-grch38.bam ├── bwa-pe-major.bam ├── bwa-se-chm13_v1.1_hg2y.bam ├── bwa-se-grch38.bam ├── bwa-se-major.bam ├── chm13_v1.1_hg2Y-grch38.clft ├── chr1_reversed_region.chain ├── del_in_indel_example.sam ├── del_in_indel_example.vcf ├── hg19.fa.fai ├── hg38ToHg19.over.chain ├── hg38_to_hg19-chr1_100216456_104974084.chain ├── major.lft ├── mm2-test1.sam ├── mm2-test2.sam ├── overlapping_example-lifted-gold.bam ├── overlapping_example.bam ├── overlapping_example.lft ├── overlapping_example.vcf ├── raw_reads │ ├── paired_end_1.fq │ ├── paired_end_2.fq │ └── single_end-cigar_op.fastq ├── simple_example.sam ├── simple_example.vcf ├── small.chain ├── spliced_example.sam ├── spliced_example.vcf ├── test_small.bed └── ultima_small.sam └── workflow ├── README.md ├── gen_genomic_annotations.sh ├── leviosam2.py ├── leviosam2.sh └── workflow-test.py /.github/actions/build-test/action.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/.github/actions/build-test/action.yml -------------------------------------------------------------------------------- /.github/actions/setup-htslib/action.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/.github/actions/setup-htslib/action.yml -------------------------------------------------------------------------------- /.github/workflows/cmake_htslib.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/.github/workflows/cmake_htslib.yml -------------------------------------------------------------------------------- /.github/workflows/integration-test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/.github/workflows/integration-test.yml -------------------------------------------------------------------------------- /.github/workflows/workflow-test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/.github/workflows/workflow-test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/.gitignore -------------------------------------------------------------------------------- /CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/CMakeLists.txt -------------------------------------------------------------------------------- /CMakeLists.txt.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/CMakeLists.txt.in -------------------------------------------------------------------------------- /INSTALL.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/INSTALL.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/README.md -------------------------------------------------------------------------------- /configs/bowtie2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/configs/bowtie2.yaml -------------------------------------------------------------------------------- /configs/default.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/configs/default.yaml -------------------------------------------------------------------------------- /configs/ont.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/configs/ont.yaml -------------------------------------------------------------------------------- /configs/ont_all.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/configs/ont_all.yaml -------------------------------------------------------------------------------- /configs/pacbio.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/configs/pacbio.yaml -------------------------------------------------------------------------------- /configs/pacbio_all.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/configs/pacbio_all.yaml -------------------------------------------------------------------------------- /docker/env/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/docker/env/Dockerfile -------------------------------------------------------------------------------- /docker/production/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/docker/production/Dockerfile -------------------------------------------------------------------------------- /docker/update_docker.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/docker/update_docker.sh -------------------------------------------------------------------------------- /figures/levioSAM_S_bw.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/figures/levioSAM_S_bw.png -------------------------------------------------------------------------------- /figures/levioSAM_S_bw_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/figures/levioSAM_S_bw_dark.png -------------------------------------------------------------------------------- /invert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/invert.py -------------------------------------------------------------------------------- /leviosam-test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/leviosam-test.py -------------------------------------------------------------------------------- /scripts/chain_invert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/chain_invert.py -------------------------------------------------------------------------------- /scripts/chain_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/chain_utils.py -------------------------------------------------------------------------------- /scripts/collect_perf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/collect_perf.py -------------------------------------------------------------------------------- /scripts/compare_fastq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/compare_fastq.py -------------------------------------------------------------------------------- /scripts/compare_sam-test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/compare_sam-test.py -------------------------------------------------------------------------------- /scripts/compare_sam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/compare_sam.py -------------------------------------------------------------------------------- /scripts/extract_seq_from_bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/extract_seq_from_bed.py -------------------------------------------------------------------------------- /scripts/extract_unpaired_reads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/extract_unpaired_reads.py -------------------------------------------------------------------------------- /scripts/fai_to_bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/fai_to_bed.py -------------------------------------------------------------------------------- /scripts/filter_bed_by_size.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/filter_bed_by_size.py -------------------------------------------------------------------------------- /scripts/gen_length_map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/gen_length_map.py -------------------------------------------------------------------------------- /scripts/get_low_identity_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/get_low_identity_regions.py -------------------------------------------------------------------------------- /scripts/get_mappable_regions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/get_mappable_regions.py -------------------------------------------------------------------------------- /scripts/leviosam_utils-test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/leviosam_utils-test.py -------------------------------------------------------------------------------- /scripts/leviosam_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/leviosam_utils.py -------------------------------------------------------------------------------- /scripts/mask_fasta_with_bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/mask_fasta_with_bed.py -------------------------------------------------------------------------------- /scripts/sam_qname_to_bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/sam_qname_to_bed.py -------------------------------------------------------------------------------- /scripts/sample_fq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/sample_fq.py -------------------------------------------------------------------------------- /scripts/summarize_aln_features.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/summarize_aln_features.py -------------------------------------------------------------------------------- /scripts/testdata/chr1_1_100000.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/testdata/chr1_1_100000.fa -------------------------------------------------------------------------------- /scripts/testdata/chr1_1_100000.fa.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/testdata/chr1_1_100000.fa.fai -------------------------------------------------------------------------------- /scripts/testdata/chr1_test1.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/testdata/chr1_test1.bed -------------------------------------------------------------------------------- /scripts/testdata/mask_fasta_with_bed-chr1_test1.fa.results: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/testdata/mask_fasta_with_bed-chr1_test1.fa.results -------------------------------------------------------------------------------- /scripts/testdata/mask_fasta_with_bed-chr1_test1.fa.results.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/testdata/mask_fasta_with_bed-chr1_test1.fa.results.fai -------------------------------------------------------------------------------- /scripts/vcf2chain.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/vcf2chain.sh -------------------------------------------------------------------------------- /scripts/vcf_to_bed.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/vcf_to_bed.sh -------------------------------------------------------------------------------- /scripts/verbosify_chain.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/scripts/verbosify_chain.py -------------------------------------------------------------------------------- /src/IITree.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/IITree.h -------------------------------------------------------------------------------- /src/aln.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/aln.cpp -------------------------------------------------------------------------------- /src/aln.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/aln.hpp -------------------------------------------------------------------------------- /src/bam.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/bam.h -------------------------------------------------------------------------------- /src/bam_aux.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/bam_aux.c -------------------------------------------------------------------------------- /src/bam_md.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/bam_md.c -------------------------------------------------------------------------------- /src/bed.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/bed.cpp -------------------------------------------------------------------------------- /src/bed.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/bed.hpp -------------------------------------------------------------------------------- /src/bed_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/bed_test.cpp -------------------------------------------------------------------------------- /src/chain.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/chain.cpp -------------------------------------------------------------------------------- /src/chain.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/chain.hpp -------------------------------------------------------------------------------- /src/chain_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/chain_test.cpp -------------------------------------------------------------------------------- /src/cigar.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/cigar.cpp -------------------------------------------------------------------------------- /src/cigar.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/cigar.hpp -------------------------------------------------------------------------------- /src/cigar_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/cigar_test.cpp -------------------------------------------------------------------------------- /src/collate.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/collate.cpp -------------------------------------------------------------------------------- /src/collate.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/collate.hpp -------------------------------------------------------------------------------- /src/gzstream.C: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/gzstream.C -------------------------------------------------------------------------------- /src/gzstream.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/gzstream.h -------------------------------------------------------------------------------- /src/ksw2.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/ksw2.h -------------------------------------------------------------------------------- /src/ksw2_extd2_sse.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/ksw2_extd2_sse.c -------------------------------------------------------------------------------- /src/ksw2_extz.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/ksw2_extz.c -------------------------------------------------------------------------------- /src/ksw2_extz2_sse.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/ksw2_extz2_sse.c -------------------------------------------------------------------------------- /src/leviosam.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/leviosam.cpp -------------------------------------------------------------------------------- /src/leviosam.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/leviosam.hpp -------------------------------------------------------------------------------- /src/leviosam_utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/leviosam_utils.cpp -------------------------------------------------------------------------------- /src/leviosam_utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/leviosam_utils.hpp -------------------------------------------------------------------------------- /src/leviosam_utils_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/leviosam_utils_test.cpp -------------------------------------------------------------------------------- /src/lift_bed.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/lift_bed.cpp -------------------------------------------------------------------------------- /src/lift_bed.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/lift_bed.hpp -------------------------------------------------------------------------------- /src/rapidyaml.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/rapidyaml.hpp -------------------------------------------------------------------------------- /src/reconcile.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/reconcile.cpp -------------------------------------------------------------------------------- /src/reconcile.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/reconcile.hpp -------------------------------------------------------------------------------- /src/reconcile_test.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/reconcile_test.cpp -------------------------------------------------------------------------------- /src/robin_hood.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/robin_hood.h -------------------------------------------------------------------------------- /src/sse2neon/sse2neon.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/sse2neon/sse2neon.h -------------------------------------------------------------------------------- /src/version.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/version.hpp -------------------------------------------------------------------------------- /src/yaml.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/yaml.cpp -------------------------------------------------------------------------------- /src/yaml.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/src/yaml.hpp -------------------------------------------------------------------------------- /testdata/HG002-0.3x-bwa-grch37-chr1_rev.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/HG002-0.3x-bwa-grch37-chr1_rev.sam -------------------------------------------------------------------------------- /testdata/HG002-0.3x-bwa-grch38-chr1_rev.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/HG002-0.3x-bwa-grch38-chr1_rev.sam -------------------------------------------------------------------------------- /testdata/bt2-pe-chm13_v1.1_hg2y.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bt2-pe-chm13_v1.1_hg2y.bam -------------------------------------------------------------------------------- /testdata/bt2-pe-grch38.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bt2-pe-grch38.bam -------------------------------------------------------------------------------- /testdata/bt2-pe-major.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bt2-pe-major.bam -------------------------------------------------------------------------------- /testdata/bt2-se-chm13_v1.1_hg2y.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bt2-se-chm13_v1.1_hg2y.bam -------------------------------------------------------------------------------- /testdata/bt2-se-grch38.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bt2-se-grch38.bam -------------------------------------------------------------------------------- /testdata/bt2-se-major.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bt2-se-major.bam -------------------------------------------------------------------------------- /testdata/bwa-pe-chm13_v1.1_hg2y.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bwa-pe-chm13_v1.1_hg2y.bam -------------------------------------------------------------------------------- /testdata/bwa-pe-grch38.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bwa-pe-grch38.bam -------------------------------------------------------------------------------- /testdata/bwa-pe-major.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bwa-pe-major.bam -------------------------------------------------------------------------------- /testdata/bwa-se-chm13_v1.1_hg2y.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bwa-se-chm13_v1.1_hg2y.bam -------------------------------------------------------------------------------- /testdata/bwa-se-grch38.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bwa-se-grch38.bam -------------------------------------------------------------------------------- /testdata/bwa-se-major.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/bwa-se-major.bam -------------------------------------------------------------------------------- /testdata/chm13_v1.1_hg2Y-grch38.clft: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/chm13_v1.1_hg2Y-grch38.clft -------------------------------------------------------------------------------- /testdata/chr1_reversed_region.chain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/chr1_reversed_region.chain -------------------------------------------------------------------------------- /testdata/del_in_indel_example.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/del_in_indel_example.sam -------------------------------------------------------------------------------- /testdata/del_in_indel_example.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/del_in_indel_example.vcf -------------------------------------------------------------------------------- /testdata/hg19.fa.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/hg19.fa.fai -------------------------------------------------------------------------------- /testdata/hg38ToHg19.over.chain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/hg38ToHg19.over.chain -------------------------------------------------------------------------------- /testdata/hg38_to_hg19-chr1_100216456_104974084.chain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/hg38_to_hg19-chr1_100216456_104974084.chain -------------------------------------------------------------------------------- /testdata/major.lft: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/major.lft -------------------------------------------------------------------------------- /testdata/mm2-test1.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/mm2-test1.sam -------------------------------------------------------------------------------- /testdata/mm2-test2.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/mm2-test2.sam -------------------------------------------------------------------------------- /testdata/overlapping_example-lifted-gold.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/overlapping_example-lifted-gold.bam -------------------------------------------------------------------------------- /testdata/overlapping_example.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/overlapping_example.bam -------------------------------------------------------------------------------- /testdata/overlapping_example.lft: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/overlapping_example.lft -------------------------------------------------------------------------------- /testdata/overlapping_example.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/overlapping_example.vcf -------------------------------------------------------------------------------- /testdata/raw_reads/paired_end_1.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/raw_reads/paired_end_1.fq -------------------------------------------------------------------------------- /testdata/raw_reads/paired_end_2.fq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/raw_reads/paired_end_2.fq -------------------------------------------------------------------------------- /testdata/raw_reads/single_end-cigar_op.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/raw_reads/single_end-cigar_op.fastq -------------------------------------------------------------------------------- /testdata/simple_example.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/simple_example.sam -------------------------------------------------------------------------------- /testdata/simple_example.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/simple_example.vcf -------------------------------------------------------------------------------- /testdata/small.chain: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/small.chain -------------------------------------------------------------------------------- /testdata/spliced_example.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/spliced_example.sam -------------------------------------------------------------------------------- /testdata/spliced_example.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/spliced_example.vcf -------------------------------------------------------------------------------- /testdata/test_small.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/test_small.bed -------------------------------------------------------------------------------- /testdata/ultima_small.sam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/testdata/ultima_small.sam -------------------------------------------------------------------------------- /workflow/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/workflow/README.md -------------------------------------------------------------------------------- /workflow/gen_genomic_annotations.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/workflow/gen_genomic_annotations.sh -------------------------------------------------------------------------------- /workflow/leviosam2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/workflow/leviosam2.py -------------------------------------------------------------------------------- /workflow/leviosam2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/workflow/leviosam2.sh -------------------------------------------------------------------------------- /workflow/workflow-test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/milkschen/leviosam2/HEAD/workflow/workflow-test.py --------------------------------------------------------------------------------