hanna
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d19366eaad
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Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1173 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-06 15:41:30 +00:00 |
kiran
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b0cc763eb5
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Added some methods to format bases such that read bases on the forward strand are in uppercase, while those on the negative strand are lowercase. This does *not* affect the default functionality of the standard PileupWalker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@969 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-10 17:31:00 +00:00 |
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kiran
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2b0e7f612b
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Handles bam pileups where some of the reads have SQ tags and some don't.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@958 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-10 08:17:15 +00:00 |
depristo
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dc17a5661d
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Better accessors for dealing with second base prob pileups
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 22:25:16 +00:00 |
jmaguire
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11723fbcc2
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added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@663 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-12 15:08:24 +00:00 |
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depristo
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5a4bb76cc3
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More capabilities for the pileup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@621 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-07 18:03:13 +00:00 |
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kiran
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4f818f5c1c
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Choose a random base to stick in the pileup if the 2nd-best base matches the best base.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@578 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-01 06:27:37 +00:00 |
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kiran
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135d3eabeb
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Now only distributes 80% of the residual probability to the secondary base, 10% each to the other two bases. Nicer labelling for stringified probability distribution output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@521 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-24 03:34:43 +00:00 |
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kiran
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5b8502745a
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Added an epsilon (1e-4) to the tertiary and quaternary base hypotheses.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@488 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-22 00:01:37 +00:00 |
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kiran
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2ac240d78b
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Removed an extraneous print statement.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@487 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 23:36:36 +00:00 |
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kiran
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0149c887ff
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Fixed a bug wherein the residual probability was not being distributed properly when a file had secondary probs and the best and next-best base agreed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@486 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 23:36:09 +00:00 |
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kiran
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dac76f041b
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Added some methods to retreive the probability distributions of individual bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@484 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 22:26:25 +00:00 |
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depristo
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72a3d84ed2
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General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:13:10 +00:00 |