depristo
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8e9e2f4502
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Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 21:06:28 +00:00 |
asivache
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55ca272919
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reimplemented; now implements Genotype interface instead of AllelicVariant
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@481 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-21 21:06:42 +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 |
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asivache
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b4136b6d6e
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a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 04:49:19 +00:00 |
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asivache
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453d13415d
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count variant as biallelic if it's just a non-ref homogeneous site!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@326 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-08 01:57:27 +00:00 |
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asivache
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8ec427ab66
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latest version... still under dev/testing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@323 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-07 22:31:06 +00:00 |