gatk-3.8

Author	SHA1	Message	Date
asivache	a009592662	the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have either reference name or reference index set for the read to be considered mapped (the flag is still checked) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1612 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-14 16:04:19 +00:00
asivache	58debd7e56	A convenience shortcut isReadUnmapped() added: thanks to SAM format specification, 'read unmapped' flag is not always required to be set for an unmapped read; this method checks both the flag and the alignment reference index/start (if those are set to '*' the flag is not required according to the spec!) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1506 348d0f76-0448-11de-a6fe-93d51630548a	2009-09-02 17:00:39 +00:00
ebanks	59f0c00d77	-set indel cleaning walkers to be in core package -move Andrey's alignment utility classes to core git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a	2009-07-24 05:23:29 +00:00