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
depristo
hanna
aaron
asivache
kcibul
kiran
jmaguire
ebanks