+ [proovbin.c,queue.h] draft implementation of proovread binning algorithm for a single bin in C; relies on FreeBSD queue.h for list implementation
- [.gitignore] added proovbin
- [proovbin.c] bin is now not only the queues head, but a struct containing the head and the bins current total length
- [proovbin.c] whitespace fixes
+ [proovbin.c] init bin in main and pass by ref to assess_aln_by_score
+ [proovbin.c] multiple bins in array
+ [proovbin.c] cleanup of assess_aln_by_score
- [proovbin.c] init bins with length 0
- [proovbin.c] trying to integrate/init bins in bwa bns (ref seq) structure
+ [proovbin.c] init and fill bins foreach seq in bwa bns ref seq structure
- [proovbin.c] renamed init_bins() to bns_bins_init()
+ [proovbin.c] added bns_bins_destroy() to cleanup bin memory; encapsuled print of bin content in bns_bins_print()
- [proovbin.c] added formula for calculating bin number based in bin size and seq length
- [proovbin.c] include "" to automatically search cwd
- [proovbin.c] typedef bin_t; renamed bin_length_max to bin_length
+ [proovbin.c,proovbin.h,proovbin_test.c,bntseq.h] created proovbin.h with defs, removed defs from proovbin.c; moved standalone testing routing from proovbin.c to proovbin_test.c; added proovbin members to bntseq_t in bntseq.h + loading and forward declaration of proovbin.h; run test: gcc -o proovbin proovbin_test.c proovbin.c && ./proovbin
- [proovbin.c] fixed minor compiler warnings
- [bntseq.h] removed unnecessary and conflicting #include "proovbin.h"
- [Makefile] added proovbin.c to bwa build
+ [bntseq.c,bwamem.c,bwamem.h,fastmap.c,proovbin.c,proovbin.h] Fully integrated assessment of scores by proovread binning, including cmd options bin_size(-b) and bin_length(-l)