Releases: cancerit/cgpPindel
v2.0.3
v2.0.0 - legacy software cleanup
- Migrates all Tabix and Bio::DB::Sam to Bio::DB::HTS::Tabix and Bio::DB::Sam
- Cleans up install
note: you will need PCAP-core v2.0+
v1.5.6 - Added fake line printed to bed file if no germline results found
- Added fake line printed to bed file if no germline results found
- Uses the first contig found and prints contig\t0\t1 as a fake entry to the germline bed file
v1.5.5 - Prevent accidental overwrite of completed work
User will encounter successful job with warning if the logs directory has already been moved to the output location.
v1.5.4 - workaround for bug in underlying code
Workaround fix for sam files with no reads causing failure in bamsort
v1.5.2 - Allow readgroups with ID=0
v1.5.1 - Correct non-absolute paths
Some paths were not being expanded which resulted in failures in later steps (#38).
v1.4.0 - Handle species with large number of contigs
This release primarily handles species where very large numbers of contigs are being analysed. If more than 100 contigs are being processed (after exclusion criteria applied) then a slower merging process is used to ensure reliable processing.
v1.3.2 - correct limit based processing
Number of required threads when using limit was not being set correctly. Generally results in needless thrashing of disk doing file checks but in some cases corrupt data or race conditions were occurring.
v1.3.1 - as v1.3.0 with correct version reported
As per v1.3.0 but version is correct (was reporting 1.2.0).