manta-1.2.2

This is a minor update from v1.2.1

Added

• Add a configurable option graphNodeMaxEdgeCount (MANTA-1247)
  • During SV candidate generation, if both nodes of an edge have an edge count higher than the configured value, that edge will be skipped for evaluation.

Changed

• Test for unsupported BAM SEQ format (MANTA-1265)
  • Test the input bam reads for use of the = symbol in the SEQ field, and provide a clear error message if this is found.
• Verify run directory has not already been configured (MANTA-1252/STREL-734/[#102])
• Update minumum boost version to 1.58 (MANTA-1250)
• Update minimum supported linux OS from Centos 5 to 6 (MANTA-1249)

Fixed

• Fix imprecise SV filtering when CIEND is a subset of CIPOS (MANTA-1146)
• Ensure consistent BND pairs for translocations or RNA fusions are selected during vcf merging (MANTA-1243)
• Fix manta to tolerate deserialization differences in boost above/below v1.58 (MANTA-1262)
  • Impact of issue was an (infrequent) assertion using boost v1.58+: Assertion 'size() == rhs.size()' failed
  • Change in boost policy for certain vectors causes vector append in some instances that were previously overwritten.
• Fix target region retrieval (MANTA-1264)
  • The bug was in retrieving overlapping subregions specified by "--callRegion" and "--region" when the argument of "--region" has chromosome name only.

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manta-1.2.2.centos6_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 6 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.2.2.release_src.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing version numbers and build system changes to improve portability.