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Arioc v1.40
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@RWilton RWilton released this 05 Nov 21:50
· 112 commits to master since this release
v1.40
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Notes for Arioc v1.40:

The current build is v1.40.2885 (1 May 2020).

This is a stable, performance-tested build.

Arioc v1.40 is not compatible with reference-genome lookup tables generated by release v1.30 and earlier. If you are upgrading to v1.40 from v1.30 or earlier, please re-execute AriocE to create new lookup tables as documented in the User Guide.

New features

  • support for NVlink GPU memory interconnect
  • more efficient concurrent use of available CPU threads
  • added performance metrics (CUDA compute capability verification, GPU memory utilization, file output timing)
  • support for circular reference-sequence topology
  • added AS (genome assembly identifier) and M5 (MD5 checksum) tags to SAM @SQ records
  • revised SAM c3 (triplet complexity score) tag to use DUST weighting and phred representation
  • reformatted tabular results to reconcile with output from samtools flagstat
  • detailed discussion of performance tuning, including previously-undocumented extra (X) parameters for fine-grained control

Bug fixes

  • AriocP, AriocU: hang (infinite loop) with certain short QNAME fields
  • AriocP: failure to recognize encoded query-sequence files (*a21.sbf) with certain multi-part filenames
  • AriocE: segfault when encoding reads with certain multi-part filenames
  • AriocU, AriocP: segfault when aligning samples that contain widely-varying read lengths
  • AriocP: data-consistency validation exception with pairs where mate 1 has multiple nongapped mappings and mate 2 is unmapped
  • AriocE: spurious error message at startup when no GPU is installed
  • AriocU, AriocP: failure to emit CPU description in certain Power9 Linux configurations
  • AriocU: duplicate mappings in SAM file with certain large-memory hardware configurations
  • AriocP: inaccurate timing of GPU-to-CPU data-transfer performance metric for nongapped mappings
  • AriocP, AriocU: updated SAM NM (edit distance) computation to conform to current SAM optional fields specification

Downloads

file content
Arioc.RQA.140.zip Linux examples
Arioc.w.140.zip Windows source code
Arioc.x.140.zip Linux source code
AriocSetup.msi Windows binaries and examples
Assets 6