quality score of a particular base is than the quality score of its neighbors. The granularity of the binning
jumps from 32 groups to 860 groups.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1702 348d0f76-0448-11de-a6fe-93d51630548a
Also, sanity check that ref is not 'N'.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1651 348d0f76-0448-11de-a6fe-93d51630548a
- summary output now reported as a percentage rather than proportion; 2 sigfigs
- fixed minor bug where FNR was calculated over total calls rather than total variant sites
- column headers are_now_contiguous_strings
- spacing fixed
- "No Call" separated from "Ref Call" as its own column
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1644 348d0f76-0448-11de-a6fe-93d51630548a
Additional output & better output formatting. It has now undergone a good five hours of testing; and for pools of size 1 outputs exactly the same statistics as GenotypeConcordance (when GenotypeConcordance is modified to do nothing on reference='N'); and for pools of many sizes outputs close to the expected (by genetics) statistics. Looks like this is working properly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1642 348d0f76-0448-11de-a6fe-93d51630548a
Deletion: PooledGenotypeConcordanceNew
Rewrite: PooledGenotypeConcordance. It works, and is blazing fast compared to the earlier version (1 order of magnitude speedup)! And is now entirely non-hackey, as opposed to before when there were some hacky bits.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1640 348d0f76-0448-11de-a6fe-93d51630548a
Iterates synchronously over two (name-ordered) single-end alignment SAM files with, possibly, multiple alignments per read and for each read name encountered returns pairs<all alignments for end1, all alignments for end2>
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1639 348d0f76-0448-11de-a6fe-93d51630548a
@PooledGenotypeConcordanceNew - a new version of the pooled genotype concordance test for Variant Eval. Code altered to be more extensible, use a private class for handling the count tables so it doesn't gunk up the code in the test itself, and for easy debugging. The hackier methods from the original were rewritten properly. Currently computes more statistics that it outputs. Code compiles, is never called by anything, and breaks none of the tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1632 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
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