7 Commits (36875fca89f1612b7cc7dd16cdda99f8876af567)

Author	SHA1	Message	Date
ebanks	bb312814a2	UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter). ... Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-16 17:28:09 +00:00
ebanks	bd2a46ab4c	I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: ... 1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis). 2. Move error checking code from rodVCF to VCFRecord. 3. More improvements to SNP Genotype callset concordance. 4. Fixed some comments in Variation/Genotype git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-13 02:52:18 +00:00
ebanks	9da5cc25ad	More archiving (with permission from Andrey) plus a move to core. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a	2009-12-03 15:40:27 +00:00
ebanks	c90bea39a1	read.getReadString().charAt(offset) --> read.getReadBases()[offset] ... [As a courtesy I fixed all instances once I was updating GenotypeLikelihoods] git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2136 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-24 04:25:19 +00:00
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