[proovread.cfg] Fixed mode ids: sr/mr+utg-noccs
- [proovread] increase samtools per thread mem and limit samtools sort threads to prevent >1024 temporary bam files for merging
- [ccseq] default dir is cwd
- [ccseq] non-fatal if no ccs reads in chunk
- [ccseq] remove bwa index files
+ [ccseq] only produce and return one consensus for all subreads of on read
+ [util/bwa,proovread,ccseq,proovread.cfg] upgrade to bwa-proovread, which implements the proovread bin-score-filter, adjusted config and calls to bwa to propagate binning related parameters accoringly
- [proovread] fixed wrong ref file in blasr utg-noccs mode
- [proovread] fixed bin size hash in proovread.cfg
- [proovread] print SeqFilter results for input reads to log
+ [proovread,proovread.cfg] added mask-min-gain-frac as fast forward cutoff: if an iteration results in less than default 2% newly masked sequence, there is no real use for another iteration
- [util/bwa] upgrade of bwa-proovread to include minor bug-fixes
+ upgrade to bwa-proovread with thread-safe bin queues