f19d7abba9
Added geli compatibility mode to SingleSampleGenotyper, to enable easy linking to the geli2popsnps.py script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@866 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 14:32:12 +00:00
4d6398cef9
a lot of people have been asking me for the equivalent of the old "PrintCoverage" command from Arachne. Even though I show them the pileup, and they agree that's more accurate/complete, they don't want to modify their scripts and/or write a translator. It was simple enough to write, so here it is.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@863 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-31 01:45:23 +00:00
c04b67c969
Basic instrumentation support for the hierarchical microscheduler.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@862 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:19:27 +00:00
c8347c3c94
set proper package name (...walkers.indels), remove couple of unused import statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@861 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:02:14 +00:00
c549c34caa
still in development and testing; kinda works
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@860 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:59:03 +00:00
c252fec1bc
synchronizing, no real changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@859 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:56:14 +00:00
eafdba7300
more efficient implementation of line parsing, runs at least 1.5 times faster
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@858 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:09:06 +00:00
8761ab3aff
Oops. IteratorPool was occasionally creating too many RODIterators in cases where some reference-ordered data was missing. Fixed by better tracking position of RODIterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@857 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:00:31 +00:00
d601548d53
added reallocate(int[] orig_array, int new_size) and int[] indexOfAll(String s, int ch); the former is self-explanatory, while the latter returns array of indices of all occurences of ch in the specified string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@856 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 20:15:00 +00:00
a1edb898ef
Make criteria for determining whether to stop and merge inputs more sane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@855 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 18:08:18 +00:00
fe3b843b65
intercept NullPointerException and rethrow it with (marginally) comprehensible error message when an attempt to get class source code location fails
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@854 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 15:56:55 +00:00
e0803eabd9
enabled underlying filtering of zero mapping quality reads, vastly improves system performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@853 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 14:51:08 +00:00
1f93545c70
Always opt to merge dictionaries when creating a SAMFileHeaderMerger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@852 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 22:38:16 +00:00
0cf90b6f8a
Tie into sequence merging code in the latest version of picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@851 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 21:48:35 +00:00
b43deda6c9
iterative changes to GLF files; also a test of checking-in over sshfs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@850 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:24:30 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
19f9ac2b05
Realign existing indels (from the aligner) to leftmost position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@848 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 04:56:51 +00:00
aa17c4a468
Farewell, functionalj. You promised much, but you could not deliver.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 01:35:49 +00:00
d275c18e58
adding some objects we need for the GLF format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@846 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:32:25 +00:00
ce6a0f522b
First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@845 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:02:24 +00:00
a11bf0f43e
Basic unit tests for ReferenceOrderedView, ShardDataProvider. Addressing GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@844 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 21:15:01 +00:00
e533c64b8f
Walker to pull out the reference for given intervals and emit them in fasta format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@843 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:39:09 +00:00
5c6163ecbf
Removing the old reads traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@842 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:36:11 +00:00
c7b032cc88
missed a file in the add.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@841 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:27:38 +00:00
3c3cd5bb64
Moving some of the data sharding around. A new shard catagory now exits, INTERVAL. This saved a lot of code that was mirroring the same approach in both the read and locus shard strategies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@840 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:24:31 +00:00
99524ab6d0
package name corrected
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@839 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:20:43 +00:00
b76f8c4eb5
moved from playground to gatk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@838 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:18:33 +00:00
c3678c7bb9
moved from playground to gatk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@837 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:18:08 +00:00
5b310e48f5
changed to use factored out Transcript class; some docs added (not much)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@836 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:17:23 +00:00
ae0bac5696
'made public' implies the 'public' keyword, actually...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@835 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:57:01 +00:00
41c1a62ac4
formerly private class, factored out and made public. Represents a transcript annotation (transcript id, genomic location, genomic intervals for all exons present in this transcript, etc)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@834 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:52:38 +00:00
8edba13ded
Unit tests for the reference views. Partially addresses GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@833 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:49:45 +00:00
9bd6489f8e
Output indels in the format appropriate for low-coverage indel submission
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@832 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:32:15 +00:00
919e995b7f
-Moved my walkers to indels directory
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-Removed entropy walker and replaced it with mismatch (column) walker
-Some improvements to the cleaner (more to come)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@830 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 16:34:24 +00:00
864a1e81e3
Delete stale class from previous rethink of the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@828 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 13:52:03 +00:00
6fab1a64fa
Started work on GLF input / output basics. Do not use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@827 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:49:59 +00:00
b81135c606
bug fixed; this rod seems to work now...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@826 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:25:34 +00:00
a488d2dbb2
Lazy creation of output streams. Only create output streams when absolutely necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@824 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:56:57 +00:00
ab7bb5800a
forgot to remove debug print statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@823 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:38:27 +00:00
568a0d3c27
exon coordinates are now parsed correctly (?). IF DELIMITER IS THE LAST CHARACTER IN A STRING, String.split() DOES NOT return empty field as the last one; instead, the last field returned will be the one immediately before such delimiter! Wicked.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@822 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:36:50 +00:00
f4119c17de
still working on it...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@821 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:07:38 +00:00
d73f2e95cc
refseq added to the list of known rod types
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@820 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:06:44 +00:00
23b7a28015
simple walker that works off pre-computed tumor/normal genotyping calls (e.g. samtools pileup). Collects overal stats and also writes somatic variants into IGV-compatible bed file if asked to. NOT finished. NOT tested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@819 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:05:47 +00:00
8f1cabd33d
cmd line args changed - again; internally uses VariantType enum
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:58 +00:00
9ef1a21112
minor changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@817 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:06 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
4edcdffe45
refseq annotation track: should be able to provide (multiple) transcript annotations available over a given genomic position. NOT finished and NOT tested!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@815 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:07:15 +00:00
149cc9989b
spaces!!!!!!!!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@814 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 19:40:25 +00:00
c2df35b7fe
- get leftmost position of indel correct
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- don't try to clean reads with mapping quality of 0
- un-deprecate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@813 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 17:24:58 +00:00
54bb643d19
Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 15:58:21 +00:00
depristo
kcibul
hanna
asivache
aaron
ebanks
andrewk