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Arioc v1.30
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@RWilton RWilton released this 24 Sep 17:16
· 132 commits to master since this release
v1.30
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Notes for Arioc v1.30:

The current build is v1.30.2559 (6 June 2019).

This is a stable, performance-tested build.

Arioc v1.30 is not compatible with reference-genome lookup tables generated by previous versions of the software. If you are upgrading to v1.30 from an earlier release, you must re-execute AriocE to create new lookup tables as documented in the User Guide.

New features

  • maximum supported genome size is now 234 base pairs (17gbp)
  • GPU-accelerated hashtable sorting in AriocE
  • lookup table sizes are 5-10% smaller than in previous versions of Arioc
  • optional MD string formatting: "standard" (strict conformance with SAM Format specification) or "compact" (saves space by omitting placeholder zeros between mismatched symbols, but incompatible with some software tools)
  • improved parsing (and faster processing) of FASTQ defline and base quality score input
  • minor changes to support Visual Studio 2019

Bug fixes

  • AriocP: incorrect POS reported for a read whose mapping overlaps the start of the reference genome
  • AriocE: unable to merge user-specified read group IDs
  • AriocP, AriocU: fully-qualified executable file path not correctly displayed
  • AriocP, AriocU: workaround for memory-allocation error handling with malloc() and realloc() in certain Linux implementations
  • AriocE, AriocU, AriocP: insufficient buffer space for very long input filenames
  • AriocP: divide-by-zero error in MAPQ computation for very short reads (~20 bases)

Downloads

AriocSetup.msi: Windows binaries and examples
Arioc.w.130.zip: Windows source code
Arioc.x.130.zip: Linux source code
Arioc.RQA.130.zip: Linux examples

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