v.0.1.19

This release adds support for the --addMateTags option. This option will cause samblaster to add MC (Mate CIGAR) and MQ (Mate Mapping Quality) tags to all SAM output lines that are associated with paired-end reads for which both reads appear in the input SAM file. The CIGAR and Mapping Quality of the primary alignment for each read are used. The MC and MQ tags are added regardless of whether both, one, or neither of the reads are mapped, and are also added to any secondary alignments associated with such a pair of reads. In addition to the main output SAM file, they are also added to the discordantFile and/or splitterFile output file(s) when specified.

These tags can be useful for downstream processing of the output SAM file(s) especially after they are position sorted, which can separate the alignments associated with paired-end reads by an indefinite distance. However, to my knowledge, no commonly used aligner includes the MC or MQ tags in their output. Therefore, it is easier for samblaster to add these tags while the file is read-id grouped than for downstream processing steps to try to access the alignment for each mate to get this information. In addition, as of now, when --addMateTags is specified, samblaster will add these tags as outlined above without first checking whether or not these tags are already present in the input file. This release is no slower than previous releases when --addMateTags is not specified. However, samblaster is a few to several percent slower when this option is used, and of course the output SAM files are also larger.

Thanks to Colby Chiang for helping to test this release.