f2f9fa3ed4
doc added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@464 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:43:25 +00:00
d639ec3776
Remove some copied code to make sure the traversal engine stays in sync with the locus context provider.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:41:56 +00:00
df5aae5ed4
got read of a couple of warnings and added percentage(x,base) methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@462 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 15:15:21 +00:00
50ae1763f7
Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:13:11 +00:00
ee5ab9536f
trivial checking / flagging issues to enable testing of merging iterator performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@460 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:11:59 +00:00
dbf2344cef
Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 01:27:36 +00:00
01be8f09e3
Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:17:25 +00:00
e5c80e59dc
fixed the case when you're not seeking, it didn't initalize
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@456 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:16:03 +00:00
f47f640df6
Better debugging output and testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 21:54:56 +00:00
165e504d1c
Turn on new TraverseLociByReference is now only dependent on the -et flag. REGION_STR does not matter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@454 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 19:45:47 +00:00
12e1f192c4
Fixed a bug in this code where it would eat reads that didn't start at the beginning of the provided interval. This should fix / help fix Kristian problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:42:00 +00:00
835f1067d8
added isHom() and isHet() queries to the Genotype interface (with the obvious meaning)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:41:39 +00:00
55537c0d1e
chnage class name, now it compiles...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@451 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:51:00 +00:00
4f9bc7206f
some cleanup, also ensuring that all reads get written into output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@450 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:49:25 +00:00
e8a6cdb386
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@449 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:46 +00:00
832afd3d60
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@448 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:27 +00:00
85308f4ddc
resurrected indel tool's standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@447 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:55:52 +00:00
6f56938d42
* added a bit more debugging output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@446 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:20:26 +00:00
d35a542bb9
* fixed bug where the merged header was not being set on the read (although the read group was)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 12:53:07 +00:00
240eb18564
fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@444 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:56:47 +00:00
0d324354ae
separate interface for genotypes as opposed to (population) allelic variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@443 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:55:16 +00:00
7e05b43f40
* added some error checking for read groups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@442 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:22:49 +00:00
56f6847456
Changed interface from contig,pos,length to more common contig,start,stop interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@441 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 00:04:41 +00:00
7261787b71
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@438 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:38:28 +00:00
e70aecf518
bug fix, but important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@437 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:07:20 +00:00
76d833e39b
Meaningful assert messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@435 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:28 +00:00
67ea66c866
Bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:18 +00:00
1edfe48194
Better debugging output with .debug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@433 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:09:18 +00:00
9cc808104e
Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers.
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Also cleaned up the debugging output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@432 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:08:26 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
339261c4a9
Load the dictionary and sanity check it against the index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@430 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:04:13 +00:00
26e84d7fd6
Added index iteration for ReferenceSequenceFile interface compatibility.
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Added better error checking for querying past the end of a contig.
Lots more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@429 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 17:17:11 +00:00
3fda8613c3
* minor formatting changes
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* support for "extended" output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@428 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 15:11:05 +00:00
12407b5b1a
Deleted the old file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:55:01 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +00:00
182626576f
Basic indexed fasta POC in place. Requires a more complete implementation of the ReferenceSequenceFile interface,
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and much more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@425 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:46:56 +00:00
7949e377e4
Intermediate commit. Refactored some simple base manipulation stuff into BaseUtils.java. Generalized some likelihood computation logic to make future possible EM-ing easier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@424 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:18:07 +00:00
d0b8d311e6
Can now optionally print the read and the alignment region of the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@423 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:10:30 +00:00
d4aaa1bef4
* fixed (with Matt's help) the argument parsing
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* outputting UCSC wiggle format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@422 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 02:17:39 +00:00
24722a442e
Slight code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:21:36 +00:00
13b0995d54
Adding an iterator that bounds the number of reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@419 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:18:31 +00:00
72a3d84ed2
General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:13:10 +00:00
baae98c6d5
and don't allocate new 200M string every time please, just pass byte array!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@417 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:55:33 +00:00
9d56355abe
bug fixed when reference name was passed as a string instead of actual reference bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:46:27 +00:00
222c4e5865
Commented out some debugging lines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@415 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:41 +00:00
49d76014d1
Commented out a debugging line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@414 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:11 +00:00
b39e584787
Primary or secondary bases that got a quality score of literally zero led to unfortunate infinities. Added an epsilon (1e-5) to every prob.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@413 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:04:49 +00:00
d28e9f9b98
search over q's for finding argmax[q] p(D|q)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@412 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:15:45 +00:00
647827b18c
Transitioned indel code to use GATK and Walkers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@410 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:15 +00:00
b363eedd2c
Deal with screwy reads by changing logic to determine whether we are
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past the last interval
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@409 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:13:16 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
186c799ffc
Class to read an .fai file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@405 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:37:18 +00:00
961dbbd4ef
Now output bases and qhat and qstar into the GFF.
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Quals coming soon (four-base)
QHAT : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 15:23:00 +00:00
dafdff1974
All bases are now indexed as A:0, C:1, G:2, T:3.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@401 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:43 +00:00
40ea22eb17
Added some methods to return the cross-talk partner base of a given base or base index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@400 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:12 +00:00
eb4b4a053b
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:19:20 +00:00
30121534ed
Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:58:28 +00:00
998fad76c6
Some utility methods for creating pileups of secondary bases and secondary quals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@397 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:57:54 +00:00
8b2c2e677b
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:43 +00:00
1cee7948ab
Added lots of assertions to check for problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@395 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:19 +00:00
794360c410
Added verbose option to show mapping qualities and base qualities as ints!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@394 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:54:48 +00:00
cc75e8f712
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:58 +00:00
11377ef390
Added lots of assertions to check for problems. The current GenomeLoc needs to be cleaned up and refactored but at least it runs. We need unit tests ASAP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@392 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:08 +00:00
bb666ce392
Added mappingQualPileup function for use in the verbose mode of Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@391 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:51:26 +00:00
bc43c0eefc
there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@390 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:47 +00:00
8e6093d5a5
remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@389 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:34 +00:00
f838a5e511
Changed some double comparisons of the form a == b to abs(a - b) <= precision. Now we shouldn't be passing or failing some if conditions due to floating-point precision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@388 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 20:05:46 +00:00
887adcfc7f
Some minor fixes to the last check-in
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:24:51 +00:00
f2d0d73309
removed old shard strategy code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@386 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:13:45 +00:00
dd604799dc
Added some new code for shard support over reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@385 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 18:11:43 +00:00
d44c30154a
added MAX_READ_LENGTH - now we can ignore long reads (454?); a bad idea in general, but the performance hit is to hard to take, at least for preliminary testing runs...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@384 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 16:53:12 +00:00
e91a429c58
A class to print out as much context about the given locus site as is possible. Useful for testing traversal engines -- run old and new code across a given region and diff the output to make sure they have the same context.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@383 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:29:55 +00:00
6652f13a17
more verbose gff output!
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EVEN MORE verbosity to come!
Tremble in anticipation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@382 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 15:21:23 +00:00
6e180ed44e
Unified caller is go.
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AlleleFrequencyWalker and related classes work equally well for 2 or 200 chromosomes.
Single Sample Calling:
Allele Frequency Metrics (LOD >= 5)
-------------------------------------------------
Total loci : 171575
Total called with confidence : 168615 (98.27%)
Number of variants : 111 (0.07%) (1/1519)
Fraction of variant sites in dbSNP : 87.39%
-------------------------------------------------
Hapmap metrics are coming up all zero. Will fix.
Pooled Calling:
AAF r-squared after EM is 0.99.
AAF r-squared after EM for alleles < 20% (in pools of ~100-200 chromosomes) is 0.95 (0.75 before EM)
Still not using fractional genotype counts in EM. That should improve r-squared for low frequency alleles.
Chores still outstanding:
- make a real pooled caller walker (as opposed to my experiment framework).
- add fractional genotype counts to EM cycle.
- add pool metrics to the metrics class? *shrug* we don't really have truth outside of a contrived experiment...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@380 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 12:29:51 +00:00
f39092526d
Added function RandomSubset
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@379 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 12:14:53 +00:00
b4136b6d6e
a few tweaks to make it more robust: ignore reads with cigars containing anything but I,D,M; don't set up contig ordering manually, rely upon reference sequence and its dictionary; don't die if a record does not have NM tag, but faal back to direct counting instead; now requires reference as a cmdline arg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@378 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 04:49:19 +00:00
756e6c61d8
Strictness args are presented as lowercase in the help, but only accepted if uppercase. Changed help to list the valid arguments in uppercase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@376 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:50:19 +00:00
c51f51f255
Make sure we always write at least 1000 points per base in each cycle's scatterplot. Print the disagreement rate between Bustard and FourBaseRecaller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@375 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:49:41 +00:00
1fb16d54e0
For SAM files that have no alignments and when no reference is specified, contigInfo.getSequence() is null, causing an error when getSequenceName() is called on the resulting null pointer. Check for null instead and return that instead of barfing here.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@374 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:48:21 +00:00
5e96ab6161
Helpful functions for converting a base (char) to a base index (A:0, C:1, G:2, T:3, alphabetical and consistent with Illumina conventions to minimize confusion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@373 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:46:23 +00:00
35fc002d5d
Debugging information is now written in such a way to make it easier to import into R.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@372 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:45:33 +00:00
6ee4fe5a20
Fixed a Bustard/Firecrest file synchronization bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@371 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:44:07 +00:00
817278be46
If a SAMRecord is on the negative strand, reverse complement the SQ tag.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@370 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:42:24 +00:00
1d5a22cacf
Extracts a Fastq file and the SQ tags to a separate file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@369 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:41:44 +00:00
e410c005c0
A debugging tool to ensure the SQ tag in a four-prob SAM file matches the SAMRecord strand orientation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@368 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 19:40:42 +00:00
c7777d46d6
* re-enabled setting of sequence dictionary information on GenomeLoc
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@366 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:44:14 +00:00
ce72932a45
* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes
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* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-12 02:25:17 +00:00
608a66e6ab
TbyLocibyRef previously didn't seem to support traversals with no interval specified. Put in a temporary fix until the threaded approach is in place.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@363 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:14:06 +00:00
c2669021b8
Cleanup, and support either by-interval traversals or full traversals in data source-backed code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@362 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 22:09:01 +00:00
2322bb7d86
Workaround: use a single ReferenceIterator for an entire micromanaged traversal. We'll have to
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do something about ReferenceIterator thread safety later.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@361 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:50:28 +00:00
95753e1b34
Should've been calling queryOverlapping in locus mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@360 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 20:22:04 +00:00
2b59110dca
CombineSamAndFourProbs is better.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@358 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:19:53 +00:00
56aa98ad30
Ignore null values.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@357 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:18:20 +00:00
2ef2c9e121
Fixed an issue wherein the SQ field was only being pulled from the first read of the pileup, no matter what. Fixed an issue wherein Andrew enumerates his bases as A:0, C:1, T:2, G:3, and Kiran's QualityUtils methods enumerate bases as A:0, C:1, G:2, T:3 (we should standardize this). Fixed an issue wherein the remaining probability was being divided by 3 rather than 2 when four-base probs are enabled.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@356 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:17:53 +00:00
17b3d5b554
New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 22:04:59 +00:00
f5cc2d8b0b
Commented out import of IlluminaParser.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@354 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:30:29 +00:00
0d825ccfc1
Oops. Fixed duplicate reference to the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@353 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:27:57 +00:00
9afa101465
Add interval support to the
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.__ __ __
_____| |__ _____ _/ |__/ |_ ___________
/ ___/ | \\__ \\ __\ __\/ __ \_ __ \
\___ \| Y \/ __ \| | | | \ ___/| | \/
/____ >___| (____ /__| |__| \___ >__|
\/ \/ \/ \/
classes!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@352 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 21:23:43 +00:00
c5220c0822
Four-base probs are now decoded with the relevant method in QualityUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@351 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:52:17 +00:00
9bc763a835
A better (aka 'working') tool for combining four-base probs with an aligned sam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@350 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:51:37 +00:00
asivache
hanna
depristo
aaron
kcibul
kiran
jmaguire
ebanks