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version 0.2.2
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@gmcvicker gmcvicker released this 15 Nov 20:25
· 144 commits to master since this release
v0.2.2
31c36a8

This release incorporates several modifications/fixes that have been made to
the master branch over the past year.

Changes include:

  • check first 2 bytes of input files to decide if they are gzipped rather than relying on .gz filename extension
  • fix bug in which unmapped reads in BAM were causing find_intersecting_snps.py to crash
  • fix bug in which some cigar codes caused find_intersecting_snps to crash because of typo in snptable
  • fix bug related to soft-clipped reads (switch to use pysam 'query_sequence' instead of 'query' attribute)
  • added check for pysam version to rmdup_pe and find_intersecting_snps.py
  • added check for pytables version to find_intersecting_snps.py
  • rescale count totals in CHT so that alpha and beta estimates stay in reasonable range
  • allow empty header lines in VCF parsing
  • change max SNP identifier length from 16 to 255
  • include much more information in output table from combined haplotype test such as SNP info, total numbers of AS reads, etc.
  • warn and gracefully handle situation where there are no matching samples on a chromosome
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