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@heilmank heilmank released this Dec 12, 2017

HSQutils v1.1 Released on: 11-Dec-2017

The most recent version of the HSQutils software user's guide can be found at the following location under “Downloads” -> ”Operators Manual”.

Bug Fixes:

  1. Fixed an issue in which some unsorted BAM files were erroneously identified as sorted.
  2. Fixed an issue in which reads were incorrectly aligned when inserts occurred between either primer and the capture target sequence.
  3. Fixed an issue in which mismatch details within the BAM file were calculated incorrectly and led to a BAM file validation error for some software tools.


  1. Updated reference to HTSJDK version 2.9.0, which necessitates the use of Java 8 for this release of HSQutils.
  2. Added logic which prevents empty attribute tags (optional fields) from being produced in the output BAM file generated by HSQutils dedup.
  3. Improved memory performance by utilizing intermediate BAM files at various steps in the deduplication algorithm.
  4. Added logic to make use of alternative mapping information when present in the provided input BAM file in the “XA” tag.
  5. Files generated by HSQutils now use a lowercase “u” in all output filenames.
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