7d889c0661
Refactored into oblivon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@276 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:12:15 +00:00
dffc879240
Should now be appropriately using Bustard data to call bases (there are some mathematical subtleties that arise when no longer using ICs as initialization data. Also writes some more relevant fields in the SAM records. WAAAAAY simpler than old version. Like, super way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@275 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:10:13 +00:00
59334b0270
A convenience class for manipulation base probability distributions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@274 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:08:31 +00:00
399d9b8c1e
A class that represents the model parameters for all of the Gaussian models for all cycles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@273 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:08:10 +00:00
f0f94b6c72
A class that represents the model parameters for all of the Gaussian models at a given cycle. Handles the accumulation of parameter initialization data and provides for efficient computation of base probability distribution.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@272 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:07:47 +00:00
a8a6c63a32
A class with some static methods that aid the manipulation of quality scores and probabilities (including a method to compress a base and quality score into a byte for SAM output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@271 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:06:15 +00:00
b7a67da775
Expose the underlying SAM reader to the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@270 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 21:38:00 +00:00
8ce4dabd7c
Print coverage per reference base for each sample in a merged BAM file.
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This is a good example for how to untangle a merged BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@269 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 21:35:31 +00:00
5d9b068b8b
generic declarations added here and there to eliminate a few annoying warnings; no consequential changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@268 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 20:53:01 +00:00
4bc035d919
half-way through making rodDbSNP implement AllelicVariant interface; does not work yet
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@267 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 20:48:59 +00:00
4faa680887
*Massive* speed-up for interval-based by-read traversals.
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[Could do more optimizing, but this simple fix was good enough for now]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@266 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 20:19:39 +00:00
c192a95998
changes in three files to make the HapMap RODs work:
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- HapMapAlleleFrequenciesROD.java - the referenceOrderedDatum implementation
- PrepareROD.java - has a static block that loads the known ROD classes, had to add the above
- GenomeAnalysisTK.java - when supplied a hapmap argument... loads the ROD
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@265 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 19:55:19 +00:00
b4cdd1d9a1
correct package name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@264 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 18:09:31 +00:00
93fc768c38
Fixing problems with SAMQueryIterator and reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@263 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 18:04:28 +00:00
d202264b23
initial add of pooled calling experiment walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@262 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 17:55:40 +00:00
3248176118
Die with appropriate error message if we try to read past the end
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of a chromosome.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@261 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 16:44:32 +00:00
24e8581c30
Slight improvements to allele caller interface; fixed problem with printing progress
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@260 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 16:44:12 +00:00
20d4bcbb2e
I said - delete!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@259 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 16:21:21 +00:00
25ace306b9
GenomeAnalysisTK: better documentation of validation option.
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AlleleFrequencyWalker: output the last reference interval if it's left hanging open.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@258 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 16:11:20 +00:00
816e768a74
move interface from playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@257 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 15:58:01 +00:00
f26055c926
interface representing allele variants/genotype calls
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@256 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 15:57:19 +00:00
f42b75da72
restore GFF_OUTPUT_FILE to a required argument.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@255 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 14:34:08 +00:00
2cd9a1597f
Simple improvements to allele caller
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@254 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 14:09:14 +00:00
d952790258
GFF now parses attributes correctly and efficiently. Slightly better interface to Utils.join
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@253 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 22:54:38 +00:00
ce57fed2fb
Hack to work around an Apache CLI bug, where core arguments couldn't be commingled with walker arguments. These arguments can commingle now. Everybody into the pool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@252 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 20:56:42 +00:00
6cc2fa24d5
Added ability to downsample to a particular coverage
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@250 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 20:27:06 +00:00
bb3dbb5756
change default onTraversalDone to use the new output streams
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@249 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 19:50:31 +00:00
4faacac315
Now handle the case where we don't actually SEE all of the positions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@248 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 19:50:07 +00:00
675505646d
now makes confident reference intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@247 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 18:46:14 +00:00
6994cca988
added precision
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@246 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 16:21:29 +00:00
16c2ea4673
Invalid arguments are not always flagged when stopAtNonOption is false. Make sure stopAnNonOption is true when we do final argument validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@245 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 15:58:57 +00:00
7ee792df04
Print correct help if core arguments (--input-file et al) aren't correctly specified.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@244 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 15:16:49 +00:00
3af4290a49
Added iterator to randomly downsample to a given fraction of the reads.
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Also, updated sort iterator to allow user to input max sorts.
Put in placeholder for downsampling to given coverage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@243 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 02:11:13 +00:00
385736469c
High performance pileup code and utilities
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@242 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 00:47:47 +00:00
ad63633b1c
forgot to change the chunks dir to shards before
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@241 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 20:28:20 +00:00
ede52f7359
- take command line arguments
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- output GFF lines to a file (specified by a command line argument)
- improve the GFF output string
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@240 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 18:43:00 +00:00
8d601a6a42
unbox
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@239 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:51:59 +00:00
234137dee8
use boolean instead of String for flag to suppress printing in map
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@236 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:14:00 +00:00
907c183242
update walkers so that onTraversalDone works (it now takes an arg)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@235 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:05:33 +00:00
3896cc8f17
Moved avg depth of coverage functionality into the core depth of coverage
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walker. Used new command line args for walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@234 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 05:02:33 +00:00
007ecc8616
Added a stateless walker to give the average depth of coverage for given reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@233 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 02:33:59 +00:00
89c1762aa9
Apparently, no one else has tried to create a stateless walker over loci until
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now, as this should have come up: make sure reduce sums get transferred to the
next reduce.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@232 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 02:31:51 +00:00
ba99e9f648
checking in some of the more static Data Source dependent code at this point. They don't do much on their own, but are need for the base data source code I'm writing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@231 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 00:04:03 +00:00
7fda409f4e
Fixed bug where read traversals would fail with an exception when not called with a genome_region (-L) argument. From TraversalEngine, line 455, looks like Mark intended an invariant where the list of locations is 0 length if not specified. Made GenomeLoc code compliant with that.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@230 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 23:43:12 +00:00
e812cfbf55
Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@229 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 23:20:55 +00:00
36f851362e
Oops. While writing command-line argument docs, I realized I introduced
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a regression in default value handling.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@226 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 18:51:39 +00:00
875802e8fc
print output as a GFF line.
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still need to add printing GFF intervals for stretches of confident reference calls.
does the GFF ROD class handle intervals?? We'll find out. >:)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@225 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 17:47:35 +00:00
b752960586
rearranged some stuff and eliminated the binomial prior in the N!=2 case. Much faster.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@224 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 17:26:05 +00:00
7c6455fe36
Handle the case where a walker is being run outside of the GATK framework, such as JUnit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@222 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 01:50:27 +00:00
d7c0bcc223
Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information.
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All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency
Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20
Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use.
Pileup now marks, very clearly, reference positions without covered reads.
Made changes around the codebase to deal with new GenomeLoc structure.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@218 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-28 20:37:27 +00:00
kiran
jmaguire
asivache
ebanks
kcibul
depristo
hanna
aaron