Improvements to the reuse_bam option with Chimerascan.  At least it runs now and skips the initial alignment.
Merge branch 'master' of ssh://git/srv/git/genome
Add SvFusionGenes.pm
Bug fix and unit test added
add unit test
More common interface change and code cleanup
More common interface change and code cleanup - missed Sv.pm
bug fixed
AQID Test: rm tests for de novo in main test script that actually did not test de novo
Completely remove GENOME_TEST_TEMP
bug fix and unit test update
Disk Alloc: in _reallocate - only getting disk usage if dir exists
updated ur submodule to 2151e28
updated jenkins submodule to 40634f5
Merge branch 'master' of ssh://git/srv/git/genome
Add reheader logic to replace the tmp chimerascan BAM (--reuse-bam=1) header with the expected Bowtie header, including each transcript contig.
reset bam-window submodule to origin/master
remove error even though thr chromosome order does need to be validated at some point.
Pass along the inputs we've declared.
Lower RAM to 16G for Picard SamToFastq