4366ce16e0
Made sure all RODs have a (good) toString() method - and use it in the Venn walker. (thanks, Mark)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 14:53:27 +00:00
feb7238f10
Wasn't always returning the correct alt base
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1337 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 03:08:04 +00:00
5429b4d4a8
A bit of reorganization to help with more flexible output streams. Pushed construction of data
...
sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1336 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 23:00:15 +00:00
7a13647c35
Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
...
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 16:11:45 +00:00
3c4410f104
-add basic indel metrics to variant eval
...
-variants need a length method (can't assume it's a SNP)!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1324 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-28 03:25:03 +00:00
f1109e9070
Added the interator to SAMDataSource to prevent seeing dupplicate reads, only in a byReads traversal. The iterator discards any reads in the current interval that would have been seen in the previous interval.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1317 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-25 22:36:29 +00:00
a361e7b342
SAMDataSource is now exposed by GATK engine; SamFileHeaderMerger is exposed from Resources all the way up to SAMDataSource, so now we can see underlying individual readers should we need them; GATK engine has new methods getSamplesByReaders(), getLibrariesByReaders(), and getMergedReadGroupsByReaders(): each of these methods returns a list of sets, with each element (set) holding, respectively, samples, libraries, or (merged) read groups coming from an individual input bam file (so now when using multiple -I options we can still find out which of the input bams each read comes from)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1315 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 22:59:49 +00:00
2024fb3e32
Better division of responsibilities between sources and type descriptors.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1314 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 22:15:57 +00:00
59f0c00d77
-set indel cleaning walkers to be in core package
...
-move Andrey's alignment utility classes to core
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1307 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 05:23:29 +00:00
0b16253db3
an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 23:59:48 +00:00
477502338f
moved major indel cleaning pieces to core (yippee!)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1301 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 19:59:51 +00:00
4efe26c59a
Major: allow genotyper to optionally output in 1KG format, including outputting the samples in which indels are found.
...
Minor: refactor 454 filtering
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1300 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 19:53:51 +00:00
ee8ed534e0
print full genotype for alt allele
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 01:35:23 +00:00
9c12c02768
AlleleBalance and on/off primary base filters -- version 0.0.1 -- for experimental use only
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1294 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-22 17:54:44 +00:00
6e4fd8db4a
Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1290 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 22:23:28 +00:00
761d70faa1
Better printing of multiple rods -- now produces a comma-separated set of values
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1289 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 21:58:27 +00:00
8588f75eb6
Better printing with toSimpleString() -- now prints out chip-genotype string
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1288 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 21:57:59 +00:00
1843684cd2
Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1287 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:50:51 +00:00
b43925c01e
Switched to Reflections ( http://code.google.com/p/reflections/ ) project for
...
inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:32:22 +00:00
436a196e2b
Bug fixes to support hapmap genotyping concordance.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1285 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 16:20:10 +00:00
f13a1e8591
adding a couple of small changes to support contract with VariantEval
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1283 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 03:49:15 +00:00
b4adb5133a
GLF rod as a AllelicVariant object.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 00:55:52 +00:00
54fce98056
duh, don't print newline
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1280 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-20 03:04:27 +00:00
1d2b545608
add FLT toString method (to be used in PrintRODs) and add it to ROD list
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1279 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-20 02:47:50 +00:00
387316ebe1
added indel rod
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1276 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 16:05:51 +00:00
da4af3b620
print indels in the format required for 1KG submissions
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1275 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 15:59:18 +00:00
d45c90b166
ROD to represent simple output from IndelGenotyper
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1274 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 14:36:12 +00:00
df1c61e049
Re-add the plugin path.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1271 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 22:48:44 +00:00
7c30c30d26
Cleaned up some duplicate code in preparation for making plugin dir configurable.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1270 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 22:02:21 +00:00
107f42a01e
Hacks for getting GLFs support in the Rod system working
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1268 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 21:03:47 +00:00
88ffb08af4
Need to return real values for some of the AllelicVariant methods
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1264 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-16 02:31:10 +00:00
ba349e8d52
add FLT ROD
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1257 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 19:40:50 +00:00
800f7e6360
make AllelicVariant extend ReferenceOrderedDatum (not Comparable) since ROD itself is Comparable. Then we can generalize RMD tags.
...
Blame Matt if this doesn't work - he said it wouldn't break anything.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1256 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 19:25:06 +00:00
5be5e1d45f
added conversion from iupac format and new rod to deal with FLT file format
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1254 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 18:34:41 +00:00
d36e232ed3
adding GLF rods to the module list
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1252 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 15:42:34 +00:00
9ecb3e0015
adding GLFRods with tests and some other code changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 15:30:19 +00:00
c25f84a01c
Regression: we lost our hack to work around BAM files with index problems (affects BAM files created before 23 Apr 2009 and traversed by interval). Added the hack back in, along with a much more explicit comment about why its there.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1248 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 14:41:37 +00:00
513d43b5f3
now implements AllelicVariant
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1246 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 14:06:25 +00:00
d369136bda
depricate this ROD yet again
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1245 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-15 13:33:03 +00:00
efcbb16688
un-deprecate this ROD and make it implement Genotype
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1240 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 19:45:41 +00:00
84d407ff3f
Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 18:53:27 +00:00
76b09a879b
Display a more intelligent error message if the user runs a locus traversal across an unmapped reads file.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1238 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 18:36:09 +00:00
99f9cd84ed
Warning for possibly mismatched reads / reference was very aggressive. Relax
...
the criteria a bit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1234 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 16:21:22 +00:00
12b5d9c70c
The number of loci can easily overflow an int. Change reduce type to a Long.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1233 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 16:07:00 +00:00
5bf7647498
0.2.3 -- now preserves Q0 bases throughout the reads
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1232 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 12:27:31 +00:00
0f6bfaaf73
Skip validation in case of no reads aligning.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1230 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 02:03:36 +00:00
bfe90af5e2
Some quick and dirty fixes to support querying unmapped BAM files.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1228 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-14 01:25:20 +00:00
9f0fb9f3aa
Fix for GSA-90: GATK banner and error messages should point to the wiki website.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1226 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 21:56:41 +00:00
b18caa2052
Fix for GSA-90: System isn't failing with an error when you use the wrong reference.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1225 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 20:42:12 +00:00
5c321f9630
Oops! Accidentally deactivated the ArgumentFactory, needed by the CleanedReadInjector, while refactoring last night.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1223 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 16:41:55 +00:00
ebanks
hanna
aaron
asivache
depristo
kiran