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NextSeq fixes
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@meren meren released this 02 Jul 17:54
· 168 commits to master since this release
v1.4.2
a06ff48

Apart from a couple of bug fixes we have two major changes in this release:

  • It seems Illumina has changed the default tile numbers. With this release the code learns tile numbers from the files, so --visualize-qual-dicts with Bokulich or Minoche filters continue generating plots with NextSeq platform as well (for which we no longer generate very very large TIFF files and go with PNG file format).
  • There are two new parameters both for iu-filter-quality-bokulich and iu-filter-quality-minoche: --limit-num-pairs (so one can test the code very fast by saying "analyze X number of reads and stop") and --print-qual-scores (which is very helpful to see what the code sees in these FASTQ files as Illumina seems to change how to report these scores).
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