8ec427ab66
latest version... still under dev/testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@323 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:31:06 +00:00
202c501939
Added a sample xml marshaller / unmarshaller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@322 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:28:16 +00:00
00722e19bc
The system now requires a dictionary file for a fasta file, or it throws an error. You can't just operate without a sequence dictionary any longer. We will transition to a GenomeLoc system that assumes a dictionary is available.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@319 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:19:54 +00:00
9c4fc633aa
Make it symmetric: if there is no sequence dictionary, also send a message to the logger, just like we do when we find the dict
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@318 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:44:39 +00:00
b64e4d1a04
seekForwardOffset changed (improved?): first, compareContigs does *not*, in general, return -1,0 or 1 if no dictionary is available; second, be more flexible in trying to jump to the right contig (current implementation of FastaFile2 will still through an exception if there's no dictionary, but iterator itself behaves transparently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@317 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:42:33 +00:00
2663ac3e4a
documentation fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@316 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 21:39:50 +00:00
8a357a88a2
right...exponential should be exponential, so I might want to increment the exponent
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@315 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 20:12:05 +00:00
6ce9e0f941
delete the old strategy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@314 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 19:40:03 +00:00
08fddd43af
-Replaced adaptive and linear strategies with an adaptive linear strategy
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-Added the exponential growth strategy
-Added factory code that allows you to transitition between strategies, so if you want to move from linear to exp at a point, and then back when you've hit a runtime threshold, it will take care of it for you.
-Changed the code to return a Shard instead of a GenomeLoc
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@313 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 19:37:38 +00:00
6369d23b43
renamed; these files are more strategy than actual shards
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@312 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 16:50:56 +00:00
e95f427965
Added isReference() to AllelicVariant and updated rodDbSNP accordingly
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@311 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 14:49:20 +00:00
99579a1ef8
Math correction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@310 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 02:18:13 +00:00
9be978e006
Intermediate commit (debugging info).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@309 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 01:20:15 +00:00
b42d8df646
the new shatter method, independent of the underlying data. The only thing needed to create a Shard is the reference seq, which may be a problem in reference less traversals, so the builder class is there so we can make different construction schemes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@308 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 00:32:57 +00:00
0baa8c0f76
We need a base exception so we can differentiate between exceptions we've generated and those external to our code. All our exceptions should extend this exception. I'll migrate the ones I can find later on.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@307 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 00:13:45 +00:00
150bca30aa
typO in the documentation...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@306 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 23:05:59 +00:00
4aa9c0d591
Matt make a good point that the Reference Iterator we were using wasn't bounded; The BoundedReferenceIterator takes a GenomeLoc to bound the iterations by
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@305 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 23:03:56 +00:00
5a5c6d1276
Added some debugging stuff (writes model parameters to one file per cycle).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@304 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 22:00:58 +00:00
0fc8a90553
removing some files from the old approach to dataSource
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@303 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 21:57:34 +00:00
5feb7ee627
temperary fix, relying on a old reference order data constructor
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@302 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 21:38:41 +00:00
af5a443e5a
add Synchronized to the has_next and next methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@301 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 21:17:11 +00:00
97d14abe85
Interface check-in for Matt
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@300 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 21:14:19 +00:00
d1c5e986d5
Another check to deal with bad reads (BWA output throws bad exceptions)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@298 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 04:58:22 +00:00
3f75fc4e83
Unfortunately, because BWA occasionally outputs crazy reads, we need
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to make sure not to have an ArrayIndexOutOfBoundsException thrown.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@297 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-06 03:51:35 +00:00
f12d40dde8
Simplified SAMRecord construction and emission.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@296 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-05 04:48:31 +00:00
0d25e71953
a declaration is made generic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@295 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-04 21:55:02 +00:00
551ce9130f
added isBiallelic() to the AllelicVariant interface and to rodDbSNP implementation. We probably don't really know how to deal with non-biallelic sites just as yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@294 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-04 21:31:16 +00:00
2e89d5e46f
That was an annoying bug to find. Mark, I want a beer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@293 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 20:05:24 +00:00
4eac3193f7
Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:54:54 +00:00
c1abcfb014
Fixed problem where we were considering reads out of order because their stop positions where out of order, but with equal starts. This involved a change in the ordering feature of GenomeLoc, which now no longer sorts by both start and stop. So as long as the start positions are equal, things are considered "in order". Perhaps this isn't a good idea to change...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@291 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:53:33 +00:00
ef06924f73
JavaDocs!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@290 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:19:17 +00:00
42eb356782
1. modifed by read traversals with indexes to be more general
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2. GenomeLocs for reads should have ends spanning the read
(moved it to GenomeLoc from Utils)
3. Got rid of those stupid unmappable characters from comments in various files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@289 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 18:24:08 +00:00
86fc18e9fc
Fixed merge bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@288 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 17:41:58 +00:00
bef475778f
- Updated --hapmap switch to --hapmap-chip to reflect the data being chip data for an individual rather than population allele frequency data in Hapmap
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- Corrected some bugs to get metrics logging working
- Added a switch --force_1base_probs to ignore 4-base probalities if they exist
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@287 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 17:32:31 +00:00
edc44807af
rod's now have names. Use getName() to access it. Next step is better interface to accessing rods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 16:41:33 +00:00
5019971290
Now outputs four-base SAM record (read name prefixed with KIR) and bustard SAM record (prefixed with BUS) for easy debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@285 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 15:48:51 +00:00
15151ac125
Corrected the use of the prior.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@284 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 15:47:47 +00:00
b854c24575
Oops. I gave this method the wrong name first time around.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@283 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 15:46:26 +00:00
9bbce32064
Basic dbSNP and HapMap frequency aware SNP caller... still in progress
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@282 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 14:24:09 +00:00
f031d882c6
ByReference traversals!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@281 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 13:23:18 +00:00
e3ac0cb500
- A lot of code cleaned up; separated metrics code from AlleleFrequencyMetricsWalker into AlleleMetrics and eliminated the former class. AFMW (aside from being a name so long that it warrants an acronym) can now be implemented by passing an option to AlleleFreqeuncyWalker that logs metrics to a file.
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- AlleleMetrics and AlleleMetricrsWalker are now ready to take a list of clasess that implement the AllelicVariant interface
- Switched a genome location in AlleleFrequencyEstimate from String to GenomeLoc which makes way more sense.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@280 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 02:09:10 +00:00
c6ab60ee04
change variable type to Boolean from boolean to make cmdline parser happy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@279 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:35:30 +00:00
16aa979e34
make -A a true flag not an argument that asks for 'true/false' value!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@278 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:23:46 +00:00
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
c2ae6765a3
Removed unnecessary dependence on playground code...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@217 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 22:48:51 +00:00
b17a03abbd
Fix argument parser test case.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@215 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 16:05:18 +00:00
cfee59e0e6
New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@214 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:40:45 +00:00
4a6be896b9
Provide out and err PrintStreams to the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@213 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:03:32 +00:00
c6d9848d08
synchronizing latest changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@212 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 14:15:44 +00:00
230c1ad161
moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@211 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 14:02:55 +00:00
826781a760
The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@210 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 13:44:46 +00:00
asivache
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