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NGLess 0.11.0

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@luispedro luispedro released this 15 Mar 04:41
v0.11.0
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luispedro Luis Pedro Coelho
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Release 0.11.0

Please use version 0.11.1 as this release introduced an important bug due to the unreliability of zstandard compression (as it manifests itself only in a small subset of inputs, it it hard to test for). The bug manifests itself in ngless exiting with an internal error. Thus, if you got results with v0.11.0, they can be trusted.

A collection of several bugfixes and performance improvements over the last few months.

User-visible improvements

  • Module samtools (version 0.1) now includes samtools_view
  • Add --verbose flag to check-install mode (ngless --check-install --verbose)
  • Add early checks for input files in more situations (#33)
  • Support compression in collect() output (#42)
  • Add smoothtrim() function

Bugfixes

  • Fix bug with orf_find & prots_out argument
  • Fix bug in garbage collection where intermediate files were often left on disk for far longer than necessary.
  • Fix CIGAR (#92) for select() blocks

Internal improvements

  • Switched to diagrams package for plotting. This should make building easier as cairo was often a complicated dependency.
  • Update to LTS-13 (GHC 8.6)
  • Update minimap2 version to 2.14
  • Call bwa/minimap2 with interleaved fastq files. This avoids calling it twice (which would mean that the indices were read twice).
  • Avoid leaving open file descriptors after FastQ encoding detection
  • Compress intermediate SAM files. In some situations this should even speed up the process as Zstandard compression is used and the process was often IO bound (#22)
  • Tar extraction uses much less memory now (#77)
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