Samtools release 1.7: markdup supplementaries, multi-region iterator * HTSlib, and so samtools, now support BAMs which include CIGARs with more than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8). * samtools quickcheck will now write a warning to stderr if it finds any problems. These messages can be suppressed with a new `-q` option. * samtools markdup can now mark supplementary alignments of reads where the primary alignment is found to be a duplicate. Supplementary marking can be turned on by passing the `-S` option to markdup. When this option is enabled, all the alignment data will be written to a temporary file so that supplementary alignments that occur before a duplicated primary can be correctly marked in the final output. The location of this temporary file can be influenced using the new `-T` option. * samtools view now supports HTSlib's new multi-region iterator. This can be enabled by passing the `-M` option to view. When using this option: - The BED filter (`-L` option) will use the index to skip through the file - Reads from overlapping regions will only be output once * samtools bedcov will now ignore BED comment and header lines (#571; thanks to Daniel Baker). * samtools collate now updates the @HD SO: and GO: tags, and sort will remove a GO: tag if present. (#757; reported by Imran Haque). * Bug-fixes: - maq2sam now checks for input files that end early. (#751; patch supplied by Alexandre Rebert of the Mayhem team, via Andreas Tille from Debian.) - Fixed incorrect check when looking up header tags that could lead to a crash in samtools stats. (#208; thanks to Dave Larson.) - Fixed bug in samtools fastq `-O` option where it would fail if the OQ tag in the input file had an unexpected type. (#758; reported by Taejeong Bae) - The MD5 calculations in samtools dict and md5fa did not handle non-alphabetic characters in the same way as the CRAM MD5 function. They have now been updated to match. (#704; reported by Chris Norman). - Fix possible infinite loop in samtools targetcut. - Building bam_tview_curses should no longer fail if a curses header file cannot be found.