Version 1.0.8

@martinghunt martinghunt released this Jan 12, 2017

bug fix: iva_qc crashes on a reference genome with no CDS. Fix added to stop iva_qc_make_db from including anthing without at least one CDS.

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Version 1.0.7

@martinghunt martinghunt released this Sep 6, 2016 · 7 commits to master since this release

Require Pysam version to be at least 0.8.1 (previously also had to be <=0.8.3 because of pyasm build issues).

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Version 1.0.6

@martinghunt martinghunt released this May 12, 2016 · 10 commits to master since this release

Two little changes, which won't affect results.

  1. Highlight the --reference option as experimental.
  2. added Travis CI.

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Version 1.0.5

@martinghunt martinghunt released this May 5, 2016 · 21 commits to master since this release

Add support for new samtools sort syntax introduced in 1.2. Keep support for old samtools versions as well.

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Version 1.0.4

@martinghunt martinghunt released this Apr 18, 2016 · 32 commits to master since this release

  • force to use pysam 0.8.1-0.8.3. The new 0.9.0 will not install.

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Version 1.0.3

@martinghunt martinghunt released this Jan 25, 2016 · 35 commits to master since this release

Now runs kmc in multi-threaded mode by default. To force kmc to use one thread, use the new option --kmc_onethread.

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Version 1.0.2

@martinghunt martinghunt released this Oct 28, 2015 · 38 commits to master since this release

  • add --test option to run on test data
  • enforce samtools version at least 0.1.19

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Version 1.0.1

@martinghunt martinghunt released this Oct 16, 2015 · 45 commits to master since this release

  • Bug fix for iva_qc_make_db --add_to_ref
  • Installation easier. Now requires pyfastaq version >= 3.10.0, which no longer depends on numpy.

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Version 1.0.0

@martinghunt martinghunt released this Jul 15, 2015 · 50 commits to master since this release

Important bug fix with libraries without overlapping reads, where contig ends were too aggressively trimmed. Defaults now handle both overlapping (ie fragment length <= 2 x read length) and non-overlapping (ie fragment length > 2 x readlength) libraries.

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Version 0.11.7

@martinghunt martinghunt released this Jul 9, 2015 · 56 commits to master since this release

Default value of max_insert changed from 500 to 800.

Bug fixes:

  • reads input file could be invalid and IVA would try to assemble anyway
  • now dies more gracefully when no contigs made.

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