1.3.3

• Excluding discordant read pair extraction if no concordant read pair distribution can be calculated.
• Fixed some contig boundry edge cases
• Ignoring reads that align outside of contig bounds
• Considering any kmer containing a base falling outside the contig bounds as unanchored
• Not adjusting bounds of assemblies over-runing contig bounds if it would result in a negative CIGAR element length
• Added configuration option to more aggressively release file handles
• Supplementary records now use the primary alignment when determining whether to extract
• Reducing intermediate file sizes by only extracting unmapped reads of interest (instead of all unmapped reads)
• Using MC mate CIGAR SAM tag if available when estimating read fragment size
• fragment size estimation now includes hard clipped bases in the base count
• Ignoring split reads that fully align to one of the split alignment locations
• improves handling split reads generated by bwa
• SV metrics calculation no longer double-counting reads
• ComputeSamTags: replaced CONVERT_SECONDARY_TO_SUPPLEMENTARY with RECALCULATE_SA_SUPPLEMENTARY parameter
• Now handling multiple independent split read alignments for a single read.
• Not setting supplementary tag on unmapped reads regardless of SA tag (prevents htsjdk validation failing)
• Now passing all common command-line arguments to child programs
• Deleting intermediate files immediately after the next step is complete
• Reduces peak disk usage