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AlgoLab / galig

A graph aligner
GNU General Public License v3.0
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make it work with Salmon 0_12_0 and unzipped fatsq #2

Closed gacatag closed 5 years ago

gacatag commented 5 years ago

The changes are based on following:

  1. Salmon 0_12_0 seems to automatically distinguish the paired reads settings when run with "-l A" parameter. No need to specify/limit to "ISF".
  2. In Salmon, the correct parameter setting for "writeMappings" seems to be "--writeMappings=SAMFILE" rather than "--writeMappings salmonSam".
  3. For unzipped fastq the run returns error. It works when these two values are set by default as: "isZipped=False" and "isFastq = False".