├── LICENSE.txt ├── README.md ├── complexsv.py ├── debreak ├── debreak_allpoa.py ├── debreak_detect.py ├── debreak_genotype.py ├── debreak_merge.py ├── debreak_merge_cluster.py ├── debreak_merge_contig.py ├── debreak_rescuedupfromins.py ├── debreak_rescuelargeins.py ├── debreak_resdup_selfalignment.py ├── debreak_writevcf.py ├── genefusion.py └── testdata ├── debreak.vcf ├── test_read.bam ├── test_read.bam.bai └── test_ref.fa /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/README.md -------------------------------------------------------------------------------- /complexsv.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/complexsv.py -------------------------------------------------------------------------------- /debreak: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak -------------------------------------------------------------------------------- /debreak_allpoa.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_allpoa.py -------------------------------------------------------------------------------- /debreak_detect.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_detect.py -------------------------------------------------------------------------------- /debreak_genotype.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_genotype.py -------------------------------------------------------------------------------- /debreak_merge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_merge.py -------------------------------------------------------------------------------- /debreak_merge_cluster.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_merge_cluster.py -------------------------------------------------------------------------------- /debreak_merge_contig.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_merge_contig.py -------------------------------------------------------------------------------- /debreak_rescuedupfromins.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_rescuedupfromins.py -------------------------------------------------------------------------------- /debreak_rescuelargeins.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_rescuelargeins.py -------------------------------------------------------------------------------- /debreak_resdup_selfalignment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_resdup_selfalignment.py -------------------------------------------------------------------------------- /debreak_writevcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/debreak_writevcf.py -------------------------------------------------------------------------------- /genefusion.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/genefusion.py -------------------------------------------------------------------------------- /testdata/debreak.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/testdata/debreak.vcf -------------------------------------------------------------------------------- /testdata/test_read.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/testdata/test_read.bam -------------------------------------------------------------------------------- /testdata/test_read.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/testdata/test_read.bam.bai -------------------------------------------------------------------------------- /testdata/test_ref.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Maggi-Chen/DeBreak/HEAD/testdata/test_ref.fa --------------------------------------------------------------------------------