- [Sam::Alignment] speed-upgrade
+ [bam2cns] added; based on sam2cns, uses samtools to access and read alignments from BAM instead of SAM
+ [samfilter] added; removes unmapped alignments from SAM, restores seq/qual of secondary alignments
+ [proovread] instead of temporary SAM, write BAM in default bwa-tasks and process BAMs with bam2cns
+ [proovread] use BAM in for shrimp tasks
+ [proovread] use BAM for blasr tasks
- [proovread] removed support for bowtie2 mapper as it does not work to well and migrating routines to BAM based consensus is not worth the effort
- [proovread] removed obsolete temporary SAM and sam2cns related variable, subs and calls
- [proovread] renamed deprecated "pbc" calls to "bam2cns"
+ [proovread] use BAM/bam2cns for read-sam/read-bam
- [siamaera,proovread] --blast-path + propagation
- [proovread] check required binaries
+ [proovread,bam2cns] scale max-cov based on sr-sampling; propagate max-cov and bin-size/utg-bin-size to bam2cns
- [proovread.cfg] assume exported samtools
- [README] minor# cosmetic changes
- [proovread] cosmetic changes to --help
- [proovread] use threads in samtools sort