8be02f6a34
Check in the omniplan file for easier sharing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@228 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 21:31:54 +00:00
20e650f397
Added examples that can be cut and pasted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@227 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 19:05:44 +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
1d972969a9
A dumping ground for information that will eventually become the GATK user manual. Currently has basic information about command-line arguments and walker output streams.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@223 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-30 16:04:30 +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
cb6a3b7e55
Bug fix: build couldn't be forced to core. Now it can be.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@221 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 01:36:25 +00:00
c4f0b4cab7
Oops. Javadoc output gets a lot cleaner when I remember to add the classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@220 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 00:29:20 +00:00
74cae62ac2
Cleaned up generation of javadoc code. Still need to fix javadoc generation to take external dependencies into account.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@219 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 00:03:08 +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
fade36a8f2
Add targets to force build to core and force build to playground.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@216 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 22:32:44 +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
d115209e86
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@209 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 13:27:04 +00:00
935a4d81c9
fixed the problem where you could specify a logging level that didn't exist
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@208 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 04:29:27 +00:00
067ae09cd0
Bump picard and samtools to latest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@207 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 02:26:28 +00:00
3abaaa3cc3
Tried to add a poor man's version of seeing all reference sites in an interval, and failed. However, I did add the command line argument and a few pieces of useful code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@206 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 00:12:35 +00:00
f7097c8ee7
Cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@205 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 21:24:12 +00:00
728f932ecf
Fix exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@204 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 20:59:32 +00:00
53fe9acf65
Make command-line arguments available in walker constructor, provide back door from
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walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 20:45:27 +00:00
1d95f06ad5
Fix path issue generating javadocs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@202 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 18:51:56 +00:00
5f9010116a
Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 16:22:35 +00:00
7cad3acc61
Support for dynamically merging data files. Preliminary only -- everything in these systems is still being tested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@200 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 14:40:50 +00:00
2808fd4bbd
Better support for required mutually exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@199 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 03:22:30 +00:00
08ece8df79
Bug fixes and support for mutually exclusive options. Still a bit rough, but will
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be easier to clean up after a walker refactoring.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@198 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 03:11:56 +00:00
f47a214f96
massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@197 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 02:26:17 +00:00
0331cd8e95
Updated AlleleFrequency* classes to calculate separate lods for VarVsRef and BestVsNextBest mixture (qstar) theories; AFWMetrics now reports single sample performance w.r.t. Hapmap chip using the appropriate lod for gentoyping (BestVsNextBest) or variant / reference calling (VarVsRef).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@196 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 02:10:18 +00:00
c88a17dfee
AlleleFrequencyWalker now can parse 4-base probs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@195 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 20:33:05 +00:00
4b7bfb284a
Support for more complex command-line types: arrays, untyped collections, typed collections, interfaces to typed and untyped collections.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@194 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 20:11:31 +00:00
9840a089ef
Added documentation for our coding standards.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@193 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 19:42:09 +00:00
2ed63fe17c
a bunch of changes that support pools.
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they don't appear to break single sample:
Allele Frequency Metrics (LOD >= 5)
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Total loci : 9000
Total called with confidence : 8138 (90.42%)
Number of variants : 11 (0.14%) (1/739)
Fraction of variant sites in dbSNP : 81.82%
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@192 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 18:52:42 +00:00
d457778283
Unified byLoci and byLociByInterval traversals. It now figures out what to do for you based on the presence of an index and set of required locations to process.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@191 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 16:01:58 +00:00
c18f8fbf5f
Documentation and cleanup of xReadLines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@190 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:36:21 +00:00
607731da91
Fixed a harmless (but annoying) bug wherein the read name for the SAMRecords increases by two on every iteration rather than one.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@189 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:20:29 +00:00
44acc358b7
Add a "notes" member to the AlleleFreqencyEstimate, e.g. for hapmap metadata.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@188 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:18:10 +00:00
d11bb0fc64
Added xReadLines class to utils. It is a iterator<string> and iterable<string> so you can easily read all lines from a file. It's been used to simplify the code to process intervals, and will be used to add merging data support to the system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@187 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:17:38 +00:00
4c29dca70d
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@186 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 09:23:42 +00:00
71d3e8e99b
fixed another bug in gapped alignment computation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@185 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 08:33:57 +00:00
40f45c2333
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 05:48:10 +00:00
8bdf49a01f
added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 03:12:54 +00:00
ff98e28abf
High-performance interval list implement -- uses StringBuilder to avoid n^2 calculation. Can handle millions of locations quickly now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@182 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 02:17:48 +00:00
30babbf5b9
Restructured AlleleFrequencyMetricsWalker to correctly report Hapmap concordance numbers for genotyping and added reporting for Hapmap reference/variant calling. Also, tiny bugfix in interval code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@181 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 01:12:05 +00:00
9e2a373184
Prototype, buggy implementation of walker command-line arguments. Doesn't
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(yet) deal elegantly with even simple cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 00:12:00 +00:00
919a86e876
Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 22:32:45 +00:00
hanna
jmaguire
depristo
asivache
aaron
andrewk
kiran