9666d47d17
ooops, debug print now removed
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3550 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 18:07:12 +00:00
4ab1f440c3
A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3547 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 16:00:22 +00:00
4a555827aa
Removing more toUpperCase sanity checks
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:38:39 +00:00
56e504789a
trivial change: toUpperCase no longer necessary
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3470 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:00:47 +00:00
7f0c638653
Fix for the indel cleaner: I forgot to "unclip" the cigar string (even though the clipped bases were removed) before using it as an alternate consensus in a particular instance.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3468 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-01 02:07:20 +00:00
cc2bf549c8
Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3455 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-28 14:10:48 +00:00
6485e8383d
Trivial change to retrigger broken build that really isn't broken
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3453 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 23:33:46 +00:00
f2e7582cfc
Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3452 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-27 23:16:00 +00:00
772f558ae0
Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.
...
Small change for Ryan to get hard-clipped reads working for the recalibrator.
PLEASE DO NOT RELEASE THIS WEEK. I still have some more testing to do and need Mark to run WG jobs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 20:04:33 +00:00
8a725b6c93
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 23:27:55 +00:00
0338345bee
Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 15:42:27 +00:00
03bea70f3a
Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-04 16:49:21 +00:00
9dff578706
Added PG tag to bam header to let people know it's been cleaned.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-30 17:30:30 +00:00
42bcca1010
Pulling out the left-alignment code for indels so that other walkers can use it.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 16:12:34 +00:00
e0b51d0df0
Trigger cleaning of duplicate reads. Also beeter debug output.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 15:12:28 +00:00
3adf7fbf64
bug fix for known-indels used as consenses
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 13:52:51 +00:00
cac125b35c
Fixed incorrect symbol printed into the output file (tag had 'R', should have had 'T')
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 16:37:28 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
...
unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
d73c63a99a
Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it.
...
Also, adding some more useful integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 05:47:17 +00:00
02a6f4c401
Moving over to VariantContext
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-15 22:07:28 +00:00
8573b0bc6f
Refactoring intervals, separating the process of parsing interval lists,
...
sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-13 15:50:38 +00:00
e7dad728df
Trivial output changes for consistency
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-07 14:47:43 +00:00
3530ef5a41
Explicit type cast fixed in order to work with new ROD implementation
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-06 15:02:56 +00:00
b4f6f54502
Reorganizing the way interval arguments are processed
...
Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java:
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java
New restrictions:
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-01 12:47:48 +00:00
3d3d19a6a7
the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.
...
a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-31 22:39:56 +00:00
47e30aba92
Rods for reads hooked up into the cleaner
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3070 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 18:17:56 +00:00
49117819f5
For the cleaner to clean, it must beat the entropy produced by the aligner (and not just the raw reads).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3068 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-24 15:21:58 +00:00
d804bdf210
New option: --maxReadsInRam . When using ON_DISK sorting option, the tool may still run out of memory in the regions of pathologically deep coverage because of the generous memory usage limit set in the underlying samtools' sorting sam writers. With this option, the user can lower the number of reads the writer keeps in memory before spilling them on disk.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2985 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-11 21:15:03 +00:00
023654696e
First pass at handling SAMFileReaders using a SAMReaderID. This allows us to firewall
...
GATK users from the readers, which they could abuse in ways that could destabilize the GATK.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2923 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-04 00:59:32 +00:00
073fdd8ec7
Let's try not to die suffocating when a bad region with humongous coverage is encountered. New option: -maxNumberOfReads (--mnr), with default of 10,000. If count of reads cached in the current window reaches the specified limit, the whole window is immediately shifted by the whole window length and all currently cached reads are dropped. NOTE: this also means that we are not going to call ANY indels from the current window, even though we could try using just the reads cached so far.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2921 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 17:34:30 +00:00
790d2a7776
adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
2010-03-03 15:56:44 +00:00
246fa28386
RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2892 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-25 22:48:55 +00:00
2572c24935
We were still dropping halves of some pairs, in which both reads were assigned to the same position. Fixed.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2885 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 23:13:23 +00:00
fef1154fc8
starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2884 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 22:11:53 +00:00
27d3ef9458
Got rid of annoying commented printouts; no functional changes
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2881 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 05:12:30 +00:00
d73bc490c2
Do not build alt consensuses from insertions that have an N in the inserted sequence. Seems to cause problems rather than solve any
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2880 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 03:00:26 +00:00
94d74d4f78
Multiple instances of the same consensus were all living happily together in the set of alt consensuses. As the result, we have been taking considerable performance hit from trying to align all reads to those instances over and over again. Fixed. Only one copy of any given alt consensus is now stored.
...
in class Consensus:
1) use Arrays.equals() to compare java arrays!!
2) if object overrides equals() it also MUST provide appropriate hashCode() (thanks, Matt)
As a side effect, a number of commented out debug prints are committed, still need them...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2879 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-24 02:09:50 +00:00
8b555ff17c
Killed the old cleaner code. Bye bye.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2868 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 20:49:58 +00:00
a640bd2d79
ignore uninteresting extended events
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2866 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 19:55:46 +00:00
32d14d988e
Overload parseIntervalRegion() to allow for the interval merging rule to be passed in (so one is not required to use the value from the GATK arg collection).
...
Now the IndelRealigner can use this functionality without being forced to merge abutting intervals (which was actually causing a problem with the cleaning).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2862 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-22 04:13:54 +00:00
bbbad79f8c
Forgot to remove debugging code
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2854 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-18 18:12:58 +00:00
7669eaaeb3
Optimizations to the cleaner algorithm; reduce total runtime by almost 20%.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2852 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-18 18:10:56 +00:00
79ab7affda
- Change sortOnDisk option to sortInMemory
...
- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-17 20:52:57 +00:00
2520889cb3
Check for bad intervals and don't emit them
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2849 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-16 21:42:36 +00:00
c6f6948f9d
Haiku:
...
Eric is a fool.
Matt found his really dumb bug.
Eric is humbled.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2830 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-12 04:51:56 +00:00
96fee7cf7a
Disabling input of known indels for use as alternate consenses. When we get rods in a read traversal, it will be trivial to hook it into the cleaner (the code is already there).
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2825 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-11 15:52:21 +00:00
a4a2c9b172
Deal with bad input; also N-way out isn't default.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2823 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-11 03:44:56 +00:00
6652b992f7
The new cleaner can now use known indels to create alternate consenses for cleaning.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2816 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-10 04:39:15 +00:00
4fe851a83d
Optimization: don't keep scoring an alternate consensus if it's already worse than the best alt seen so far.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2806 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-07 05:06:32 +00:00
asivache
ebanks
depristo
hanna
bthomas
aaron