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
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
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
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
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
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
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
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
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
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
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)
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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%
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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
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
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
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
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
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
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
b7a2e82b46
Can optionally process raw or corrected intensities.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@349 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:50:11 +00:00
6cdad10dd1
Make output type identical to the bustard parser so the values can be easily swapped for one another.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@348 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:49:34 +00:00
d0ce56e018
Remember to take the strand flag into account when calculating error rate per cycle as a surrogate for instrument performance.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@347 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 20:48:45 +00:00
c556a97f17
Skeleton of Somatic Coverage tool
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@342 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-09 02:34:03 +00:00
089bf30cf4
Send things to the out file via the logger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@339 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 21:49:03 +00:00
6db9a00a0b
SAMFileWriter doesn't appear to flush the buffer when its destructor is called. You have to call the close() method. Also, choose a random base for Ns in the forward and reverse strands so that samtools doesn't pitch a fit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@338 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 21:48:24 +00:00
eb2f0ebd62
If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:58:18 +00:00
0e7d962eca
Oops. Slight twiddle of the math here so that I'm not asking if bestBase == nextBestBase.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@336 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 19:56:54 +00:00
asivache
kcibul
kiran
depristo
jmaguire
ebanks