2953c9f069
Efficiency improvement requested by the Picard team in IndexedFastaSequenceFile: improve the memory efficiency
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(and loading time) of long reference sequences by better controlling the input buffer size.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3665 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 07:22:07 +00:00
300a18b85f
Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually.
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Note that this functionality will only work if the directory with the fasta is writeable. GATK will fail if directory is read only and and either the .fasta.fai or .dict files don't exist. In the future, we could have these references be created in memory, but we decided against it this time.
Locking was also added to ReferenceDataSource so no issues come up while running multiple GATKs on the same reference: we don't want one process to be half-finished and another try to read it. So, you could see error messages related to locking. See ReferenceDataSource.java for explanation of the locking strategy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3601 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-21 21:42:42 +00:00
db1383d0b2
Rev the latest version of Picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3575 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-16 23:55:07 +00:00
99b684ea89
Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3527 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-10 20:10:23 +00:00
930082314a
Put a major.minor version into the GATK Javadoc for reading. Also,
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update some straggler packages to the new package-info.java format introduced in 1.5.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2604 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-15 21:48:30 +00:00
9e2f831206
A bit of cleanup in preparation for Picard patch.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2286 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-08 16:09:04 +00:00
8fbc0c8473
fix for bug GSA-234: fasta index files couldn't handle anything but letters, numbers, or spaces in the contig name
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2147 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-24 19:19:47 +00:00
85a4fbc256
Bumping version of Picard for firehose compatibility.
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Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1864 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-16 19:38:56 +00:00
32d55eb2ff
Fix issue Eric was seeing with java.lang.Error in unmap0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1804 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 17:46:56 +00:00
f4b6afb42c
JVM issue id 5092131 ( http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131 )
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was causing OOM issues with the new mmapping fasta file reader during large jobs.
Temporarily reverting the reader until a workaround can be found.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1801 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 04:45:46 +00:00
fcb6a992c8
Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than
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the loop-with-small block size. Performance improvements in loading refs are extreme;
segments can be loaded in <1ms. chr1 in its entirety can be loaded in 1.5sec (down
from 30sec).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1781 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 00:07:15 +00:00
2e4949c4d6
Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 20:37:59 +00:00
60a86fb34a
Better handling of fasta files with non-standard extensions.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1206 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-09 18:18:48 +00:00
433ad1f060
Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 18:49:08 +00:00
d4d3af20f2
made a fake fasta generator, so we can now generate a complete bam / fasta combo of made up data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1150 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 21:35:34 +00:00
43a28750e0
Package level documentation -- helps new users get acclimated to the codebase more quickly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1029 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 16:27:48 +00:00
78b7fb25c7
allow contig names to have spaces in the fai. This is not yet supported by samtools fai generator (which truncates at the first space), but we might as well fix it on our side.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1022 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:23:12 +00:00
fc7320133c
Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@867 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:34:38 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
d35e20ce21
Better error checking for missing .dict file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@741 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 21:57:12 +00:00
67293168e7
Support periods in sequence names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@715 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 20:17:57 +00:00
e50ae97fe1
Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:40:21 +00:00
45d962e491
I understood the contig index incorrectly when I initially wrote this code. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@517 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 22:31:43 +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
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
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
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
hanna
bthomas
aaron