2. Fix ratio printouts (for params file)
3. Rename ratio filter's get counts method to avoid confusion; more changes on the way this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1616 348d0f76-0448-11de-a6fe-93d51630548a
don't print out intervals to be merged if they're not within the global -L intervals
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1615 348d0f76-0448-11de-a6fe-93d51630548a
@NQSMismatchCovariantWalker - Walks along the gene calculating the table
# NQS
# Q score
# mismatches at non-dbsnp sites
# total number of bases at non-dbsnp sites
And prints it out at the end.
Changes:
@PooledGenotypeConcordance now works. Takes a path to a file listing a bunch of hapmap IDs in whatever pool we want to check, reads those in, and checks for concordance by name.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1614 348d0f76-0448-11de-a6fe-93d51630548a
but mostly altering the code so it's much more readable and understandable, and much less hacky-looking.
ADDED:
@Quad: This is just like Pair, except with four fields. In the original CoverageAndPowerWalker I often used
a pair of pairs to hold things, which made the code nigh unreadable.
@SQuad: An extension of Quad for when you want to store objects of the same type. Let's you simply declare
new SQuad<X> rather than new Quad<X,X,X,X>
@ReadOffsetQuad: An extension of Quad specifically for holding two lists of reads and two lists of offsets
Supports construction from AlignmentContexts and conversion to AlignmentContexts (given
a GenomeLoc). There are methods that make it very clear what the code is doing (getSecondRead()
rather than the cryptic getThird() )
@PowerAndCoverageWalker: The new version of CoverageAndPowerWalker. If the tests all go well, then I'll remove
the old version. New to this version is the ability to give an output file directly
to the walker, so that locus information prints to the file, while the final reduce
prints to standard out. Bootstrap iterations are now a command line argument rather
than a final int; and users can instruct the walker to print out the coverage/power
statistics for both the original reads, and those reads whose quality score exceeds
a user-defined threshold.
CHANGES:
@PoolUtils: Altered methods to accept as argumetns, and return, Quad objects. Added a random partition method
for bootstrapping.
@CoverageAndPowerWalker: Altered methods to work with the new PoolUtils methods.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1602 348d0f76-0448-11de-a6fe-93d51630548a
Rollback of Variant-related changes of r1585, additional PGC code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.
@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.
@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.
Added:
@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution. However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
1. VariantsToVCF can now be called statically to output VCF for a single ROD instance; this is temporary until we have a VCF ROD.
2. VariantFiltration now outputs only 2 files, both mandatory: all variants that pass filters in geli text, and all variants in VCF.
If there are any problems, go find Aaron.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1569 348d0f76-0448-11de-a6fe-93d51630548a
2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N'
3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1568 348d0f76-0448-11de-a6fe-93d51630548a
andrewk
hanna
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