first working (using test data) implementation of the bam slicer
added a step to create index for the input BAM if one does not exist already
made extracting missing mates perl script more stringent to avoid false reads
adjusted samtools option to include unmapped ends who mates are in capturing regions
tweaks to handle corner cases properly, avoid reads being double captured
further tweaking
bug fix in the new perl script
make test huge bam quicker by avoid copying the bam
added a small test bam
minor update to workflow, added sam filter script and test bam
Merge branch 'feature/junjun_bam_slicer' of github.com:SeqWare/public-workflows into feature/junjun_bam_slicer
deleted redandunt test bam file
Merge branch 'develop' into feature/junjun_bam_slicer
merged from brian_workflow_2.5 branched. Fixed the conflict by overwriting edit to the workflow_decider.pl on the develop using brians branch
uncommented download part to use to launch_and_monitor_gnos.pl
change the default test GNOS analysis object for testing
added steps to extract unmapped reads and their mates and upload it to a different GNOS object
minor changes
minor bug fix
added md5 calculation for bai file, updated gnos_upload_data.pl with specific metadata for bam slicing etc