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Release 1.7 created by Rob Davies on 26 January 2018, 12:12:22 UTC 
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.

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