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Version 1.3.1
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@snayfach snayfach released this 20 Aug 16:28
· 12 commits to master since this release
v1.3.1
4c7a06b

Changes to read alignment mode for snps and genes

  • Switched back to global Bowtie2 read alignment in run_midas.py snps. This makes the program consistent with versions <= 1.2.2.
  • run_midas.py genes module has always used local alignment, so there are no changes here
  • Added option -m in run_midas.py to choose between global and local read alignment. For example, you can now runs the snps module using local alignment: run_midas.py snps /path/to/indir -1 /path/to/fastq -m local --aln_cov 0.75. This command will recapitulate the behavior of v1.3.0.
  • Addresses issue #66
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