├── COPYING ├── Makefile.am ├── README.md ├── configure.ac ├── git-version-gen ├── m4 └── acx_pthread.m4 ├── quip-format.md ├── quip.1 ├── src ├── Makefile.am ├── ac.c ├── ac.h ├── assembler.c ├── assembler.h ├── bloom.c ├── bloom.h ├── crc64.c ├── crc64.h ├── crc64_table_be.h ├── crc64_table_le.h ├── dist.c ├── dist.h ├── dist_impl.c ├── dist_impl.h ├── dist_template_off.h ├── dist_template_on.h ├── fastqfmt.c ├── fastqfmt.h ├── idenc.c ├── idenc.h ├── kmer.c ├── kmer.h ├── kmerhash.c ├── kmerhash.h ├── make_qualenc_prior.py ├── make_seqenc_prior.py ├── misc.c ├── misc.h ├── qualenc.c ├── qualenc.h ├── quip.c ├── quip.h ├── quipfmt.c ├── quipfmt.h ├── quiplib.c ├── sam │ ├── COPYING │ ├── bam.c │ ├── bam.h │ ├── bam_aux.c │ ├── bam_endian.h │ ├── bam_import.c │ ├── bgzf.c │ ├── bgzf.h │ ├── khash.h │ ├── kseq.h │ ├── kstring.c │ ├── kstring.h │ ├── sam.c │ ├── sam.h │ ├── sam_header.c │ └── sam_header.h ├── samfmt.c ├── samfmt.h ├── samopt.c ├── samopt.h ├── samoptenc.h ├── seqenc.c 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