Merge branch 'hotfix/find' into develop
Merge branch 'hotfix/warnings' into develop
Output XP tag to annotate the end of secondary alignments - required as we do not output CIGAR strings for secondary alignments
Stable sort matches by errors
Removed single-end match selector, paired-end selector works on initialized primary matches list
Added random match picker, removed getFirstMatch() and countValidMatches()
Pick primary single-end alignment among co-optimal matches at random, pick primary paired-end alignment among co-optimal matches by minimizing insert deviation
Removed an unused type
Added matches function removeSuboptimal()
Fixed a regression in sorting due to a typo in getSortKey()
Count mapped reads - as ctx is not used in all-mapping
Merge branch 'feature/pairs' into develop

* feature/pairs:
  Count mapped reads - as ctx is not used in all-mapping
  Fixed a regression in sorting due to a typo in getSortKey()
  Added matches function removeSuboptimal()
  Removed an unused type
  Pick primary single-end alignment among co-optimal matches at random, pick primary paired-end alignment among co-optimal matches by minimizing insert deviation
  Added random match picker, removed getFirstMatch() and countValidMatches()
  Removed single-end match selector, paired-end selector works on initialized primary matches list
  Stable sort matches by errors
Merge branch 'develop'

* develop:
  Count mapped reads - as ctx is not used in all-mapping
  Fixed a regression in sorting due to a typo in getSortKey()
  Added matches function removeSuboptimal()
  Removed an unused type
  Pick primary single-end alignment among co-optimal matches at random, pick primary paired-end alignment among co-optimal matches by minimizing insert deviation
  Added random match picker, removed getFirstMatch() and countValidMatches()
  Removed single-end match selector, paired-end selector works on initialized primary matches list
  Stable sort matches by errors
  Output XP tag to annotate the end of secondary alignments - required as we do not output CIGAR strings for secondary alignments