109bef6c08
We're no longer in the read-dropping business.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
4d880477d6
Deal with ends of contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@900 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 20:09:53 +00:00
40bc4ae39a
The building blocks for segmenting covariate counting data by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@899 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 19:55:24 +00:00
13be846c2a
qualsAsInt argument for Pileup -- fixing stupid bug [again]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:52:12 +00:00
97c8ff75dd
qualsAsInt argument for Pileup -- fixing stupid bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:51:17 +00:00
9de3e58aa8
qualsAsInt argument for Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:37:39 +00:00
4d654f30d4
slightly improved error message printed upon failure to parse interval list file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@895 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:24:43 +00:00
bcc7bacba1
added List<Transcript> getTranscripts(); also more comments added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@894 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 16:25:14 +00:00
b492192838
Pairwise SNP distance metrics now enabled
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@892 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 00:11:29 +00:00
8672ae6019
Now seeing results from the training data. There are still some critical problems in the quality of the output, but we're at least getting training output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@891 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 20:41:07 +00:00
4e41646c88
print out stats for Andrey
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@890 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 17:45:35 +00:00
dfe464cd81
Updated CovariateCounterWalker to be read group aware
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@889 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 10:06:06 +00:00
40af4f085c
Adding some utilities to test unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@887 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 07:40:34 +00:00
fa93661133
Eric wins the prize for pointing out that doubles weren't valid command-line arguments. Made all primitive types parseable as command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@884 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 22:41:10 +00:00
107b5d73b5
The flagStatReadWalker generates the exact same statistical output as the samtools flagstat command, so the two outputs can be diff'ed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@883 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 21:23:56 +00:00
a1218ef508
changed default value for failure output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@880 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 19:32:29 +00:00
7e7c83ddca
fixing insidious bugs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:33:45 +00:00
6e60cddfed
A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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e. Really a stopgap; error handling in the RODs needs to be addressed in a more comprehensive way. Right now, hasNext() isn't guaranteed to be correct.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@878 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:14:46 +00:00
ad5b057140
parameterized a bit more
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@877 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 17:58:26 +00:00
587d07da00
Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@876 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 16:55:05 +00:00
82aa0533b8
added some more documentation to the GLF writer and it's supporting classes, and some other fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@875 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 14:53:58 +00:00
c4cb867d74
basic clustering of reads to reduce artifacts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@873 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 02:54:21 +00:00
e712d69382
GLF writing support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@872 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 21:30:18 +00:00
417f5b145e
Strand test and misc touch-ups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@871 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 17:13:21 +00:00
fc91e3e30e
equals signs can be important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@870 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 16:56:21 +00:00
4edb33788b
added a fix for a bug Andrew found
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@869 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 16:53:56 +00:00
b7defeae83
Fix bug in unit tests created by new filter in TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@868 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:50:44 +00:00
fc7320133c
Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@867 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:34:38 +00:00
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
008d677bea
Fixed ValidatingPileup to work with Andrey's new rodSAMPileup -> GenotypeList type hierarchy.
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Fixed reference-ordered data validation system to validate class hierarchies instead of specific class types.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-23 20:50:28 +00:00
d056f9f3e8
Changed the name to reflect the sorted nature of the set, added some fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@810 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 22:34:24 +00:00
831d430025
Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:52:40 +00:00
34413362fd
Bugfix: handle case where queue is empty.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@808 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:45:22 +00:00
ec2e8d5726
Fixes for getting ValidatingPileup running in parallel.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:20:24 +00:00
cd80e3f372
Replaced dumb training function with a version that creates a training set slightly more sensibly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@806 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:34:33 +00:00
02c0afdb85
Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@805 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:33:34 +00:00
454a6d1df7
Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:32:20 +00:00
2a5be1debe
Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:12:00 +00:00
02fc4f145f
refactoring: a couple of general purpose (hopefully useful?) methods/classes extracted into a standalone utils class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@802 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 18:54:40 +00:00
4b718688d5
no changes, really, just synchronizing (instead of reversing) to increase the amount of entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@801 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:27:28 +00:00
893f1b6427
updated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@800 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:50 +00:00
a9dfbfb309
internal changes and some refactoring. slightly different final report. Now can take tracks that implement either Genotype or GenotypeList; takes an arg specifying what variants to look for (POINT - aka snp - or INDEL); takes an arg specifying whether default ref/ref call of one type (INDEL/POINT) should be implicitly assumed if another call (POINT/INDEL respectively) was made at the same position [this is probably most useful for indels and only (?) for sam pileups: if we have only point mutation call at a given position, it does mean that we do have coverage, and that there was no evidence whatsoever for an indel, so we have an implicit 'no-indel' call]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@799 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:09 +00:00
d5bb4d9ba9
Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@798 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:20:01 +00:00
732fed9aad
ALERT, ALERT! rodSAMPileup is now a GenotypeList, not a Genotype! Now it can intelligently read full samtools pileup files (containing, in general, both point and indel genotypes at the same position). No need to split/synchronize pileups from different individuals anymore, hooray!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@797 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:17:59 +00:00
26633957d9
Genotype interface is extended: now it requires implementing object to be able to tell whether it isPointGenotype() or isIndelGenotype() (and the contract requires, e.g. alleles to be represented differently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@796 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:14:46 +00:00
d9fc84f1e3
actually checking in the first pass
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@795 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:13:27 +00:00
8773b3a430
a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@794 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:12:01 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
f2ea193149
For some reason the apostraphes in the comments were throwing annoying
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compile-time warnings: "unmappable character for encoding UTF8"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 14:07:07 +00:00
9902ce8073
properly flush the gzip output stream. this was a subtle inheritance bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:57:58 +00:00
63caca31bf
minor update in report printout format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@790 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:56:09 +00:00
aaron
ebanks
hanna
depristo
asivache
andrewk
kcibul
jmaguire
kiran