Releases: bcgsc/biobloom
Releases · bcgsc/biobloom
Public Release of Github Repository
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