cleaned up; can view alignemnt data fairly nicely (still needs justification right)
cleaned up; can view alignement data fairly nicely, but still needs justification right
trivial
Merge branch 'develop' into qcChipSeqFlow
modifiedBwaMergeSortDedpupTasklet.java to ALWAYS generated an alighment stat.txt file
merged with blessed - still has new change to BWAMergeSortDedupTasklet.java and will now be tested on barcelona
Merge branch 'develop' into qcChipSeqFlow
added alignerSpecificBamTagIndicatingUniqueAlignment as a grep string for getting unique aligned reads
Merge branch 'develop' into qcChipSeqFlow
Merge branch 'develop' into qcChipSeqFlow
Merge branch 'develop' into qcChipSeqFlow
Merge branch 'develop' into qcChipSeqFlow
Merge branch 'develop' into qcChipSeqFlow
Merge branch 'develop' into qcChipSeqFlow
Merge branch 'develop' into qcChipSeqFlow
fixed bug in getUniquelyAlignedNonRedundantReadCountCmd
hope for thebest
Merge branch 'develop' into qcChipSeqFlow
moving along with replicateSets for chipseq
further movement on the capturing replicates