Mauricio Carneiro 9ea40f2e41 Deletions/Insertions in hard clip and bug fixes ... * Deletions now count as hard clipped bases in order to recover the original alignment start of a clipped read. * Insertions do not count as hard clipped bases for the same reason. * This created a bug in the previous cigar cleaning function. Fixed.		2011-09-23 16:37:08 -04:00
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R	Merge branch 'master' into sgintervals	2011-09-19 09:50:19 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	…
doc	…
java	Deletions/Insertions in hard clip and bug fixes	2011-09-23 16:37:08 -04:00
packages	Fix the AnalayzeCovariates packaging.	2011-09-22 11:55:40 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Updating the MDCP	2011-09-22 11:27:40 -04:00
testdata	Adding bgzip vcf file for unit tests	2011-09-21 15:39:45 -04:00