├── .gitignore ├── Makefile ├── README.md ├── blockjoin.c ├── blockjoin.h ├── cli.c ├── cli.h ├── example ├── output.mp.bam ├── output.mp.bam.bai ├── output.mp.gtf ├── output.mp.vcf ├── phased.bam ├── phased.bam.bai └── variants.vcf.gz ├── ketopt.h ├── khashl.h ├── ksort.h ├── kstring.c ├── kstring.h ├── kthread.c ├── kthread.h ├── kvec.h ├── main.c └── main_test.c /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/.gitignore -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/README.md -------------------------------------------------------------------------------- /blockjoin.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/blockjoin.c -------------------------------------------------------------------------------- /blockjoin.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/blockjoin.h -------------------------------------------------------------------------------- /cli.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/cli.c -------------------------------------------------------------------------------- /cli.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/cli.h -------------------------------------------------------------------------------- /example/output.mp.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/output.mp.bam -------------------------------------------------------------------------------- /example/output.mp.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/output.mp.bam.bai -------------------------------------------------------------------------------- /example/output.mp.gtf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/output.mp.gtf -------------------------------------------------------------------------------- /example/output.mp.vcf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/output.mp.vcf -------------------------------------------------------------------------------- /example/phased.bam: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/phased.bam -------------------------------------------------------------------------------- /example/phased.bam.bai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/phased.bam.bai -------------------------------------------------------------------------------- /example/variants.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/example/variants.vcf.gz -------------------------------------------------------------------------------- /ketopt.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/ketopt.h -------------------------------------------------------------------------------- /khashl.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/khashl.h -------------------------------------------------------------------------------- /ksort.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/ksort.h -------------------------------------------------------------------------------- /kstring.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/kstring.c -------------------------------------------------------------------------------- /kstring.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/kstring.h -------------------------------------------------------------------------------- /kthread.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/kthread.c -------------------------------------------------------------------------------- /kthread.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/kthread.h -------------------------------------------------------------------------------- /kvec.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/kvec.h -------------------------------------------------------------------------------- /main.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/main.c -------------------------------------------------------------------------------- /main_test.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nanoporetech/pomfret/HEAD/main_test.c --------------------------------------------------------------------------------