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manta-1.2.0
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@x-chen x-chen released this 28 Sep 01:52
· 373 commits to master since this release
v1.2.0
fc54af5

This is a major feature update from v1.1.1. The release includes

  • The improved iterative assembler being the default assembler
  • Several improvements in calling RNA-seq data
  • A couple of new features including contig output for DNA data and specification of an existing alignment stats file
  • A few improvements in providing more specific messages to users
  • A number of bug fixes

Full ChangeLog:

Added

  • MANTA-696 Improve the iterative assembler and set it to the default assembler
  • MANTA-1207 Add an optional feature to output contig in vcf
  • MANTA-1215 Add an option for specification of an existing alignment stats file
  • MANTA-1043 Add more read statistics when 'too few read pair observations' exception
  • MANTA-886 Add verification of the extension of alignment input file
  • MANTA-1118 Add QC check of read length
  • MANTA-1044 Enable build on more architectures
  • MANTA-1231 Enable clang5.0 build

Changed

  • MANTA-445 RNA: Select contigs for refinement based on alignment score and read count
  • MANTA-443 Improve the check of running into adapter for data with small insert size
  • MANTA-1177 Improve CRAM reference handling
  • MANTA-1041 Improve exception message context to include associated read and SV candidate info
  • MANTA-1116 Sort duplicate vcf entries together to allow merging

Fixed

  • MANTA-1211/[#99] Fix issue with empty regions input to EstimateSVLoci
  • MANTA-1038 Fix infrequent graph edge lookup failure
  • MANTA-1175 Fix a bug of duplicate RG & PG in evidence bams
  • MANTA-865 Fix sortVcf.py to handle vcf files without a header

Please note that starting from this release, the linux binary distribution is built on CentOS 6.

manta-1.2.0.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-1.2.0.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.

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