cc75e8f712
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:58 +00:00
ce72932a45
* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes
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* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:25:17 +00:00
12752cf893
Added a bunch of fixes: MSRI wasn't working, sharding had broken edge cases, and SAMBAM DS needed to close the file handles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@341 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 00:20:15 +00:00
d4ab95c098
Added a constructor, took out a copy constructor, and changed some SAMBAM code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@335 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:53:20 +00:00
b64e4d1a04
seekForwardOffset changed (improved?): first, compareContigs does *not*, in general, return -1,0 or 1 if no dictionary is available; second, be more flexible in trying to jump to the right contig (current implementation of FastaFile2 will still through an exception if there's no dictionary, but iterator itself behaves transparently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@317 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:42:33 +00:00
150bca30aa
typO in the documentation...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@306 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 23:05:59 +00:00
4aa9c0d591
Matt make a good point that the Reference Iterator we were using wasn't bounded; The BoundedReferenceIterator takes a GenomeLoc to bound the iterations by
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@305 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 23:03:56 +00:00
af5a443e5a
add Synchronized to the has_next and next methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@301 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 21:17:11 +00:00
42eb356782
1. modifed by read traversals with indexes to be more general
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2. GenomeLocs for reads should have ends spanning the read
(moved it to GenomeLoc from Utils)
3. Got rid of those stupid unmappable characters from comments in various files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@289 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 18:24:08 +00:00
93fc768c38
Fixing problems with SAMQueryIterator and reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@263 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 18:04:28 +00:00
3248176118
Die with appropriate error message if we try to read past the end
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of a chromosome.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@261 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 16:44:32 +00:00
3af4290a49
Added iterator to randomly downsample to a given fraction of the reads.
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Also, updated sort iterator to allow user to input max sorts.
Put in placeholder for downsampling to given coverage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@243 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 02:11:13 +00:00
d7c0bcc223
Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.
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All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-28 20:37:27 +00:00
c2ae6765a3
Removed unnecessary dependence on playground code...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@217 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 22:48:51 +00:00
d115209e86
moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@209 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 13:27:04 +00:00
3abaaa3cc3
Tried to add a poor man's version of seeing all reference sites in an interval, and failed. However, I did add the command line argument and a few pieces of useful code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@206 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 00:12:35 +00:00
7cad3acc61
Support for dynamically merging data files. Preliminary only -- everything in these systems is still being tested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@200 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 14:40:50 +00:00
6df19ab793
Support for byInterval traversals for Jared. Do not use them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:55:34 +00:00
9f500215da
Support for reseting the system; Cleanup later
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@174 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:52:11 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
depristo
kcibul
aaron
asivache
ebanks
hanna