2235245af0
PrivatePermutations generalized to compute transition counts and average probabilities (and thus was renamed). Changes in some pipelines to reflect the change. Bugfix in the batch merging pipeline (it would halt because the allele VCF for genotyping batches could become off-spec).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4894 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 15:16:15 +00:00
2217837845
Commit for Khalid -- should be a scala version of vcf2table but for some reason the run method isn't getting called.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4841 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 00:44:15 +00:00
f36861eeee
One more little bfix -- the issue was not the grep command, but instead the NFS in the awk; i changed it to ++count in the last commit which was really responsible for the fix. Then this ultra-escaping semi-broke teh grep again.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4831 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 20:36:14 +00:00
d34c5640d2
Bugfix for clf version of extract samples. Due to dynamic shell creation and bsubs and whatnot, the OR pipe for grep ("a|b") needs to be super-escaped ("a\\\\\\\\|b").
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4829 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 19:06:30 +00:00
f795b25c47
In-process versions of sample extraction and interval-list conversion for VCF files. Required an in-process-function branch of the queue library.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4827 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 17:36:53 +00:00
7bc2049031
Updates and bug fixes to private mutations qscript and pipeline libraries. Hand filter strings are now not busted (boo to having to escape quotes); convenience method added to VariantCalling to propagate standard trait data to a given GATK command line -- should be made more scala-esque in the future.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4824 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-13 04:55:13 +00:00
cf75caf653
java changes:
...
VariantEvalWalker's logger is made public, so that variant eval modules can access it through the parent object.
DesignFileGenerator comment lists how best to bind things to it, and the feature accessor is better refined to grab the genome loc. (old change)
scala changes:
convenience addAll( List[CommandLineFunction] ) added to QScript class (and thus removed from the fCPV2)
useful command line functions added to a new library package for command line functions (these are fast simple VCF command lines)
bug fixed in ProjectManagement for the class where there's only one batch to be batch-merged (not really part of the use-case, but an edge-condition that came up during pipeline testing)
first draft of a private mutations pipeline which will be elaborated in future
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4823 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-12 05:10:45 +00:00
81290d238d
Restructuring my qscripts
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4821 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-11 20:58:45 +00:00
c19f567424
Sometimes, inputs are really outputs in disguise.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4631 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-05 19:51:16 +00:00
0e40321a52
Brütall hack: make the bam list creator job wait for the interval creator job, so that there is an implicit dependency of UG on the interval list, by way of the bam list
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4628 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 20:43:11 +00:00
cb0b2f9811
My analysis script for private mutations. I'm committing it because it contains a number of specialized command line functions that could prove useful in the future. (For example: ConcatVCF and ExtractSample)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4626 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-04 19:57:27 +00:00
chartl