96972c3a5c
a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly.
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Also moved a buch of Lists over to Sets for consistancy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 04:57:50 +00:00
a69ea9b57c
Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially.
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also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 04:11:34 +00:00
b82c3b6040
Better error output (and fixed spelling mistakes)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1857 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 01:01:45 +00:00
993c567bd8
I had to remove some of my more agressive optimizations, as they were causing us to get slightly different results as MSG. Results in only small cost to running time.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1856 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 00:59:32 +00:00
7d7ff09f54
throw an exception if read has no associated read group
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1855 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 18:11:32 +00:00
b9544d3f89
Output formatting change (very slight)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1854 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 16:47:29 +00:00
839c5d66bc
Read uints directly into longs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1853 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 16:15:11 +00:00
ce38fa7c81
Breaking the signed int glass ceiling; stage 1: convert critical ints to longs. Code cleanup and documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1852 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 15:28:56 +00:00
79993be46c
changed blank gene name to UNKNOWN
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1851 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-15 13:47:00 +00:00
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
6d7f4481e4
Changed traversal type slightly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1800 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 04:11:48 +00:00
a9f3d46fa8
Your time has come, SSG.
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Fare thee well.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1799 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 20:27:56 +00:00
8fdb8922b8
now output in the exact format that works with sequenom software.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1798 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 20:06:27 +00:00
98e3a0bf1a
VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 19:50:04 +00:00
95f24d671d
Fixed 'visualization' of reads that didn't match bwa's alignments exactly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1796 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 19:45:30 +00:00
29ad6cd876
Made redundant by BCMMarkDupes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1795 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 18:47:20 +00:00
94d82d1915
Matthew Bainbridge's duplicate removal utility for 454 data. This code should eventually be moved into a read walker. For now, it's being introduced into the repository as-is (well, with one minor change to make the handling of command-line arguments a little more straightforward).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1794 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 18:32:37 +00:00
15bf014e0b
logger.info -> logger.debug (don't want to risk filling up my log on genome-wide calls)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1792 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:53:11 +00:00
df8ea8f437
UG integration test. This was the old SSG test with MD5s updated.
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I'll need to add some multi-sample tests in a bit...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1791 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:43:58 +00:00
008455915a
One way of making the integration test stop failing is to remove it...
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[waiting for Matt to cringe...]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1789 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:08:41 +00:00
f89a89ffe3
Use of AlleleFrequency as an input to PowerAndCoverage is deprecated by the new walker. Reverting to the standard "power at 1 allele" calculation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1788 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 16:07:45 +00:00
ae05f5c7ad
Fixin the header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1787 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 15:49:28 +00:00
11ff1e09b8
A new power walker for the user to feed in a number of alleles. Call that number k. Output is:
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Locus Power_for_k_alleles Power_for_k-2_alleles Power_for_k-2_alleles ... Power_for_1_allele
This was a request from Jason Flannick & the T2DB group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1786 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 15:35:35 +00:00
04fe50cadd
*** We no longer have a separate model for the single-sample case. ***
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For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input. For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.
The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you. More on that in a separate email.
Other minor cleanups added too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 14:08:57 +00:00
32128e093a
misc. changes to get the numbers back to the baseline while keeping the speedup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1784 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 12:27:07 +00:00
d38a0d04b9
fix a snp mask offset error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1783 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 12:25:40 +00:00
829e99413b
Rescores a variant after removing duplicates (defined very strictly as reads with the same start points).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1782 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 03:07:36 +00:00
fcb6a992c8
Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than
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the loop-with-small block size. Performance improvements in loading refs are extreme;
segments can be loaded in <1ms. chr1 in its entirety can be loaded in 1.5sec (down
from 30sec).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1781 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 00:07:15 +00:00
02d2492d68
Simple tool for picking sequenom probes for SNPs. Can be extended to indels if necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1780 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 23:46:41 +00:00
1905b5defa
Hash by chromosome for now to reduce memory. This is a temporary solution until we decide how to reture the Injector for good.
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Also, with Picard's latest changes, we need to make sure we don't double-close the sam writer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1779 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 20:06:25 +00:00
f9a1598d75
Reformatting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1778 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 20:03:34 +00:00
203c626fc2
A wrapper around the GenotypeLikelihoods class for the UnifiedGenotyper. This wrapper incorporates both strand-based likelihoods and a combined likelihoods over both strands.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1777 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 19:57:37 +00:00
5bdcc2b4dc
Included HLA class 2 genes in CreatePedFileWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1776 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:46:51 +00:00
8f896b734f
Included HLA class 2 genes in CreatePedFileWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1775 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:28:01 +00:00
f9a0eefe4b
GELI_BINARY is now functional, and can be used as a variant type in SSG (-vf=GELI_BINARY). Also fixed the max mapping quality column in both GELI output formats, we haven't been correctly outputing up until now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1774 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:20:34 +00:00
225b9bccc1
Modifications to NQSClusteredZScoreWalker to output empirical mismatch rates on bins by both Z-score and reported Q-score, rather than averaging over all Q-score bins for each Z-score.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1773 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 13:45:12 +00:00
8dd0924b37
Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1772 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 23:40:30 +00:00
4554ca1b28
more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1771 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 19:09:27 +00:00
3aec76136f
Removing the AllelicVariant interface, which is replaced by the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 17:44:24 +00:00
1bd0c3c145
variant eval allows non Variation rod objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1768 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 13:04:26 +00:00
66fc8ea444
GSA-182: Adding support for BED interval files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 02:45:31 +00:00
aec83b401d
SSG multithreading doesn't play well with some I/O changes made since I last svn up'd. Reverting until I can find the reason.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1766 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 19:48:57 +00:00
8a503c86b6
Code supporting SSG proof-of-concept shared memory parallelism.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1765 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 18:56:16 +00:00
fb619bd593
-Refactoring: make GenotypeCalculationModel constructors empty so that they don't have to be updated every time we add a new parameter; instead put that logic in the super class's initialize method (making everything protected so that only the factory can access them)
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-Adding initial version of Multi-sample calculation model. This still needs much work: it needs to be cleaned up and finished. Right now, it (purposely) throws a RuntimeException after completing the EM loop.
Also:
-Fix logic in GenotypeLikelihoods.setPriors
-Add logger to the models for output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1764 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 18:10:36 +00:00
98076db6b4
Modified CreatePedFileWalker to output PED file given HLA allele names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1763 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 03:06:42 +00:00
56bc4fa21a
Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-04 18:20:20 +00:00
05aa928e3e
Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1761 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-03 21:55:18 +00:00
7605ee500c
Idiocy! All tests were being disabled because I forgot the instanceof
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1760 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 20:04:56 +00:00
88d0890cc3
Made PooledGenotypeConcordance a standard test in VariantEval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1759 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 20:03:31 +00:00
7fc4472e6d
A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).
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Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 19:35:35 +00:00
68cb2ee54b
Tweaks to parameters for NQS analysis walkers; change to PowerAndCoverage for Jason Flannick (can input the number of alleles to compute power for - i.e. doubletons, tripletons; rather than statically checking singletons.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1757 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 19:11:27 +00:00
aaron
ebanks
asivache
chartl
hanna
kcibul
depristo
jmaguire
kiran
sjia