depristo
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7cad3acc61
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Support for dynamically merging data files. Preliminary only -- everything in these systems is still being tested
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@200 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-26 14:40:50 +00:00 |
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depristo
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d457778283
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Unified byLoci and byLociByInterval traversals. It now figures out what to do for you based on the presence of an index and set of required locations to process.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@191 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 16:01:58 +00:00 |
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depristo
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d11bb0fc64
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Added xReadLines class to utils. It is a iterator<string> and iterable<string> so you can easily read all lines from a file. It's been used to simplify the code to process intervals, and will be used to add merging data support to the system...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@187 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 15:17:38 +00:00 |
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depristo
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8bdf49a01f
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added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 03:12:54 +00:00 |
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depristo
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ff98e28abf
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High-performance interval list implement -- uses StringBuilder to avoid n^2 calculation. Can handle millions of locations quickly now
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@182 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 02:17:48 +00:00 |
andrewk
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30babbf5b9
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Restructured AlleleFrequencyMetricsWalker to correctly report Hapmap concordance numbers for genotyping and added reporting for Hapmap reference/variant calling. Also, tiny bugfix in interval code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@181 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 01:12:05 +00:00 |
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depristo
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919a86e876
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Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 22:32:45 +00:00 |
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depristo
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6df19ab793
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Support for byInterval traversals for Jared. Do not use them.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 20:55:34 +00:00 |
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andrewk
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9dee9ab51c
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Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@163 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 03:58:03 +00:00 |
hanna
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63cd1fe201
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Push core / playground lower into the tree.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-23 23:19:54 +00:00 |