0c2016c19a
Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1850 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 12:07:44 +00:00
a9094c835c
clean-up and fixes to the VCF input
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1849 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 04:53:59 +00:00
a32470cea1
Deal with the fact that walkers can call UG's init/map functions directly.
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We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 02:31:45 +00:00
8dca236958
Base-packed reader cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1847 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 01:26:23 +00:00
316b30ee56
On the road to human: make sure the suffix array will fit in a Java array.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1846 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 21:45:35 +00:00
e740e7a7ce
Because walkers call UG's map function, we need to move the actual writing out
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to UG's reduce function.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1845 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 20:49:26 +00:00
825e6c7a4d
added calculation for bases over 2x,10x,20x,30x plus gene name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1844 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 20:32:26 +00:00
727b69fce0
catch null output destinations earlier
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1843 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 20:07:15 +00:00
1f66738c8e
Fix a hashing function bug. Ignore reads with non-reference bases in the pileup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1842 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 19:41:26 +00:00
72c34f11dd
Bug fixing for BWA output formats.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1841 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 19:32:22 +00:00
60183229ab
the oldest java mistake in the book...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1840 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 19:32:13 +00:00
52d2e0ca07
All walkers now use read.getReadGroup()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1839 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 19:27:40 +00:00
0a09fa4d5c
Rename to distinguish this transition table calculator from the scala version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1838 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 18:52:21 +00:00
1d055011bd
Getting rid of this so I can rename it without the world blowing up.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1837 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 18:45:11 +00:00
eb90e5c4d7
changes to VCF output, and updated MD5's in the integration tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 18:42:48 +00:00
89771fef05
-Use read.getReadGroup()
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-Add another filter for read groups for Chris
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1835 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 18:08:32 +00:00
311ab8da5a
A helper class to create the masks for the sequenom design maker.
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This project is now officially done.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1834 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 17:28:51 +00:00
3553fc9ec0
Preparing for human -- support bwa output files directly rather than relying on a custom fixed sa interval.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1833 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 17:17:46 +00:00
d89bc2c796
This class no longer outputs in sequenom format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 17:16:36 +00:00
0c95d6906f
Merge both versions of the Sequenom assay design maker: use Jared's base code and add in indels. [Jared, this still emits the same output for SNPs as your original version)
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Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1831 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 17:11:45 +00:00
49af5269e5
Jared: feel free to change or revert, but until we move over to UG version...
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Only print out positions with at least one non-ref call
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1830 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 17:08:57 +00:00
f5a2e6dd50
Fix!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1829 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 16:15:20 +00:00
f2886d88e0
We now emit genotype calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1828 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 02:49:56 +00:00
1b214c0de5
Fixed logic: throw exception if contigs are NOT equal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1827 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 02:48:44 +00:00
aeca14d052
On our side of 5CC, we spell multi M-U-L-T-I.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1826 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 01:41:25 +00:00
c9c8fd1fef
Added the discovery LOD score to the meta data
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1825 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-14 01:24:06 +00:00
0c06bf9dbc
Explicitly set output to GELI now that default is VCF
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1824 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 22:12:03 +00:00
a76fac4687
Cleanup existing speedups. Minor performance improvements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1823 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 21:51:18 +00:00
837ae1d33a
Optimization: from 22k reads/min - 30k reads/min.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1822 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 20:59:29 +00:00
96b8499a31
Remodeled version of the UnifiedGenotyper.
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We currently get identical lods and slods as MultiSampleCaller (except slods for ref calls, as I discussed with Jared) and are a bit faster in my few test cases. Single-sample mode still emulates SSG.
The remaining to do items:
1. more testing still needed
2. we currently only output lods/slods, but I need to emit actual calls
3. stubs are in place for Mark's proposed version of the EM calculation and now I need to add the actual code.
More check-ins coming soon...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1821 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 20:27:01 +00:00
b28446acac
Multi-sample calls now have associated meta-data (SLOD, allele freq), which wil
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l soon actually be used...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1820 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 20:08:43 +00:00
db642fd08b
Optimization: from 10k reads/sec - 22k reads/sec..
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1819 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 18:07:15 +00:00
77499e35ac
fixes for GSA-199: Need easier way to write binary outputs to standard output. GLF and VCF now have stream constructors, and can get dumped to standard out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1818 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 15:50:20 +00:00
f37564e63a
Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1817 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 15:50:04 +00:00
8d0e057d83
I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure
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I have previous revision to revert back to.
This is a calculator that will calculate:
P[ True base is X | read base mismatches, secondary base is Y, previous K bases are Z1,Z2,...ZK ]
where the number of pervious reference bases to take into account is user-defined. The secondary base is optional as well.
--usePreviousBases k
tells the walker to use the k previous reference bases in the transition table
--useSecondaryBase
tells the walker to use the secondary base at a locus in the transition table
these can be used together.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1816 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 02:55:29 +00:00
be92a1e603
Don't try to close if the lazy initialize hasn't triggered
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1815 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-13 01:20:25 +00:00
ec83bc6ec5
This somehow didn't make it into subversion the last time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1814 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 21:11:13 +00:00
ecbb11e017
Modified PowerBelowFrequency to ignore reads below a user-defined mapping quality. Request from Jason Flannick.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1813 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:59:24 +00:00
ec68ae3bc5
Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1812 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:58:37 +00:00
0d73fe69e7
Recalibrator by NQS. Had this puppy running all afternoon. Thing had got through 100,000,000 reads before I decided to delete my sting tree. *sigh*, a little more delay.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1811 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:55:02 +00:00
ee0afba0af
Recalibration stuff...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1810 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 20:51:39 +00:00
caf689821f
added method to get normalized posteriors
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1809 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 02:33:22 +00:00
cf7a26759d
-use the getReadGroup() function that was added to picard for us
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-clean up some include lines
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1808 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-12 01:39:32 +00:00
d844d1c496
SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1807 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 19:16:46 +00:00
da084357db
Fixed minor typo in output message.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1806 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 18:56:54 +00:00
62c484b57a
Fixes for GSA-201, where enumerated types in command line arguments had to be defined as all uppercase for the system to work.
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Also a little playground walker that changes the sort order flag of a BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1805 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 18:11:32 +00:00
32d55eb2ff
Fix issue Eric was seeing with java.lang.Error in unmap0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1804 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 17:46:56 +00:00
9f3482ef11
VCF is both a multi- and single- sample format, so we shouldn't be throwing an exception when used for SS
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1803 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 17:43:26 +00:00
d9f5a314ac
avoid an out of memory error by no putting more than 5000 reads in the cache. on pilot1 at least those are crazy loci anyway.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1802 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 14:56:55 +00:00
f4b6afb42c
JVM issue id 5092131 ( http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131 )
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was causing OOM issues with the new mmapping fasta file reader during large jobs.
Temporarily reverting the reader until a workaround can be found.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1801 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 04:45:46 +00:00
depristo
aaron
ebanks
hanna
kcibul
chartl
jmaguire