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Releases: bcgsc/biobloom

Public Release of Github Repository

16 Jul 23:27
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Many options added and bug fixes with respect to Public Release 2.0.6

biobloomcategorizer:
New Options:
-c Ordered filtering:

  • Prioritize filters in order listed in options
  • Will speed up program when using multiple filters when expecting reads to hit a single filter
  • With this option multimatch will be empty
  • May increase specificity when using multiple filters

-d printing of reads that hit a specified filter to stdout:

  • Useful for pipelines to perform analyses on the fly or purposely not output reads to disk to minimize IO

-l sequence length threshold

  • Will not consider reads shorter than threshold if set

-i inclusive paired end mode

  • Allows for single read matches in when using paired end read mode
    -w with score in multimatch

Changes:
-s

  • if set to 1 will become max score mode and will print score to best filter's header (NOTE* - Not working, known issue as of March 09 2016, however this is fixed in latest version)

Minor performance improvements

biobloommaker
New Options:
-r Progressive filter creation

  • Creates a filter recruiting reads from a paired end read set using seed sequence.
    -i inclusive mode for progressive filter
  • Allows single read matches when recruiting reads with -r

Changes:
Minor fixes to bloom filter size and number of elements calculation
Fixed bug when parsing input fasta file where sequence is the same length as k-mer size