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”.
- Fixed an issue in which some unsorted BAM files were erroneously identified as sorted.
- Fixed an issue in which reads were incorrectly aligned when inserts occurred between either primer and the capture target sequence.
- 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.
- Updated reference to HTSJDK version 2.9.0, which necessitates the use of Java 8 for this release of HSQutils.
- Added logic which prevents empty attribute tags (optional fields) from being produced in the output BAM file generated by HSQutils dedup.
- Improved memory performance by utilizing intermediate BAM files at various steps in the deduplication algorithm.
- Added logic to make use of alternative mapping information when present in the provided input BAM file in the “XA” tag.
- Files generated by HSQutils now use a lowercase “u” in all output filenames.