d603145cb0
Meaning of input arguments has CHANGED: minFraction is now a minimum fraction of CONSENSUS indel observation, out of all reads covering the site, required to make the call. minConsensusFraction is still the minimum fraction of CONSENSUS indel observation out of all indel observations at the site
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1160 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 20:38:10 +00:00
62807139fc
Cleanup pileup and depth of coverage in preparation for release. Add pileup, depth of coverage, and print reads to package for distribution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1159 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:54:01 +00:00
6a25f0b9c5
refactored into new package
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1158 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:37:54 +00:00
1c83b4d949
forgot to take out some test code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1157 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:18:37 +00:00
bc17ff567a
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 14:15:50 +00:00
47cb9f169e
Stable tool that's the reverse of merging -- splits a file into individual BAM files, one for each sample ID in the SAM header
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1155 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 12:56:46 +00:00
6684cb8bc9
copySamFileHeader() utility function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1154 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 12:55:51 +00:00
bb92eb8b1c
added a fix for overlapping reads in the locus context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1153 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-02 02:08:59 +00:00
d4d3af20f2
made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 21:35:34 +00:00
c2e5a68aaf
output format changed in --verbose --somatic mode: now also prints the <#reads with indels>/<coverage> for normal samples, rather than only for the tumor; also, code cleaned up a little
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1149 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:56:16 +00:00
4cbf069de1
First version of coverage evaluation tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1148 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:52:25 +00:00
7462f3f344
Bug in setContig() fixed: sequence dictionary's .getSequences().contains() and .getSequences().indexOf() do NOT work when applied to contig names (Strings), since getSequences() returns a list of SAMSequenceRecord's; changed to querying the dictionary directly for specified contig name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1147 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:50:09 +00:00
76fd4b3848
deal with different contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1146 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 19:17:27 +00:00
20fab507a8
Choose the REF if it scores equal to consensus!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1145 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:54:27 +00:00
9b182e3063
Prep for documenting command-line arguments: delete some arguments that don't make sense any more given
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the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 18:23:35 +00:00
5a5103cfd2
Heads up, everyone: command-line args no longer need to be public.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1143 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 16:09:22 +00:00
b43d4d909e
Fix CleanedReadInjectorTest to work with new CleanedReadInjector.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1142 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 15:48:06 +00:00
d58eeb7539
Don't cry wolf: only one warning is now emitted, instead of tons of warnings.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1139 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 13:50:37 +00:00
a3e0ec20c4
Kill the TraverseByLocusWindows traversal. TraverseLocusWindows will take its place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1138 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 13:46:35 +00:00
93da64db10
Update naming for consistency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1136 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 22:03:21 +00:00
e93f751bd7
First step in replacing the Hello, World! document. Revamped the HelloWalker and checked it into the source tree, created a special build file for it, and added it to the packaging tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1135 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 21:59:54 +00:00
8d3dc57c3d
Commit to emit in sorted order so we don't have to use /tmp
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1133 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:47:15 +00:00
f5cba5a6bb
Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:17:24 +00:00
177d6d00b8
added setContigIndex(). NOTE: both setContig() and setContigIndex are UNSAFE as one does not automatically involve updating the other, and there's also no validation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1130 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 17:40:37 +00:00
9fca79ed62
Read groups are now sorted in the output data, for convenience
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1129 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:50:44 +00:00
08df4771c8
count X/N/etc. as mismatches for the NM attribute in the BAMs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1127 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:08:55 +00:00
d412c5dc2f
Updated to use SecondaryBaseAnnotator class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1126 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:08:43 +00:00
e3cdf7ef4b
A single class that can be handed reads for training and basecalling. When in training mode, we accumulate no more than 10000 reads and always replace the lowest-quality reads with superior quality reads. Thus, the training set always contains 10000 of the best reads available. After training is complete, the class can be interrogated to return the SQ tag for a given RawRead object.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1125 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 16:03:15 +00:00
8aa3b65e7f
fix to guarantee emission in sorted order
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1122 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 13:48:41 +00:00
03f8177a53
When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:51:55 +00:00
1dcababad1
a fix to make the test run
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1120 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 20:24:32 +00:00
a17bf145f6
fix to respond to the change in IndelLikelihood constructor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1119 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 19:05:33 +00:00
7ecc43e9a7
Fixed subtle null ptr exception discovered by Kiran. Now deals with the rare situation where you have only say Q28 bases at dbSNP sites, so you fail in the Table recalibration step with a null pointer error into the data structure indexed by quality score. If you are Q score above those seen before you aren't modified in any way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1118 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 18:57:42 +00:00
95e2ae0171
Deal with reads whose ends are aligned off the end of a chromosome.
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Includes update to ignore non-ATCG bases (not just 'N')
(Also, create a BWA dir for future work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1117 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:50:05 +00:00
65a788f18a
Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls.
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Some doodling around with indel calling in an EM context.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1116 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:32:12 +00:00
ceeeec13b8
Computes a vector of numbers of reads falling into successive intervals of specified length (e.g. numbers of reads per every 1Mbase)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1115 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-29 16:12:21 +00:00
eb74b16e39
updated what constitutes removing entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1113 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 18:29:00 +00:00
d7d4298917
Some files to support generic genotype outputing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1112 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:43:41 +00:00
1a97c86f95
don't crash when an unmapped read is encountered, just write it into the output file, it should be ok
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1111 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-26 15:33:59 +00:00
491ed70b44
TraverseByLocusWindow -- asstd bug fixes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1109 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:51:38 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
73caf5db15
This is, strictly speaking, NOT a GATK module. Standalone, picard-level executable except that it uses couple of gatk utils (GenomeLoc). Remaps alignments from cutom reference (such as transcritome, hyb-sel etc) onto the 'master' reference
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1107 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:04:18 +00:00
ee2af3b423
I committed this too soon... reverting...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1106 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:49:12 +00:00
ad3a3aa350
First pass at passing lists of files / lists of interval arguments work. Note that the interval
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ROD system will throw up its hands and not deal with intervals at all if multiple interval files
are passed in (see JIRA GSA-95).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:44:23 +00:00
23680a9a16
Replaced an expensive sort with an inexpensive direct computation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1104 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:25:12 +00:00
83816fb801
Stop using the annoying refIterator (temp change until new traversal is green lighted)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1103 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 20:05:39 +00:00
0c3aabd1c5
logger output should be less verbose by default. Also fixed a printout in my read validation walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1102 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 19:47:29 +00:00
11d83ac7d0
pushing up to test on unix box
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1101 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 19:00:48 +00:00
0d9041380d
remove printouts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1100 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:54:14 +00:00
0a16519aa2
a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 18:30:32 +00:00
asivache
hanna
kcibul
aaron
depristo
andrewk
ebanks
kiran
jmaguire