specify the version of pysam
contig ids and number of read pairs should be of integer type
number of bases in gaps should never exceed (100 - min percent identity)% of the length of query
command lines should be interpreted with bash
awk scripts for filtering blat PSLs for redundancy removal
incorporate the filtering of PSLs with awk scripts for redundancy removal
improved reference path extension using dist info
provide the paths of awk scripts to filter PSLs for redundancy removal
1. Provide the paths of awk scripts to filter PSLs for redundancy removal. 2. Use dist file to improve the extension of the final reference paths.
Merge branch 'master' of https://github.com/bcgsc/transabyss
skip the removal of predecessors from start of path and successors from end of path
specify specific gmap version