2403e96062
Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs.
2011-10-21 09:59:24 -04:00
110e13bc1e
Merge branch 'master' into SamRecordFactory
2011-10-21 09:43:52 -04:00
be797a8a1f
Recalibrator now uses the much more efficient NGSPlatform in the cycle covariates system
2011-10-21 09:39:21 -04:00
ed74ebcfa1
GATKSamRecords with efficiency NGSPlatform method
2011-10-21 09:38:41 -04:00
94e1898d8f
A canonical set of NGS platforms as enums with convenient manipulation methods
2011-10-21 09:37:45 -04:00
999a8998ae
Constructor for GATKSamRecord with header only, for unit testing
2011-10-19 17:51:48 -04:00
bba69701b5
Now creates GATKSamRecords now SamRecords
2011-10-19 17:49:17 -04:00
cd8a6d62bb
You know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that.
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This commit contains:
- IntronLossGenotyper is brought into its current incarnation
- A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate)
- RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type.
+ the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there.
- MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added)
+ use this rather than a hard GQ threshold if you're doing MV analyses.
- Some miscellaneous QScripts
2011-10-19 17:42:37 -04:00
52345f0aec
Meaningful documentation string
2011-10-19 15:47:36 -04:00
1b38aa1a7e
Cleaning up reduced read code accessors
2011-10-19 15:46:44 -04:00
d8d73fe4f2
Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown.
2011-10-19 15:11:13 -04:00
7928b287fc
GATKSamRecord now produced by SAMFileReaders by default
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-- Removed all of the unnecessary caching operations in GATKSAMRecord
-- GATKSAMRecord renamed to GATKSamRecord for consistency
2011-10-19 13:15:27 -04:00
5a6468c11e
Allowing ./X genotypes and adding a unit test to ensure that this case is covered from now on (especially given that we may want to revert in the future). Reverting this change is really easy and entails uncommenting a few lines of code. But for now, despite Mark's objections, this case is allowed in the VCF spec and we are wrong not to allow it.
2011-10-19 11:52:05 -04:00
48c4a8cb33
Make error messages clearer (even I was confused)
2011-10-19 11:49:16 -04:00
6cadaa84c9
Just use validate() from super class since it does the same thing
2011-10-19 11:48:23 -04:00
df3e4e1abd
First working code to use SamRecordFactory to produce objects of our own design in SAMFileReader
2011-10-19 11:22:35 -04:00
c27e2fb676
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-18 15:23:05 -04:00
f77f2eeb7d
Fix for new ID structure
2011-10-18 13:04:43 -04:00
1a92ee3593
No longer adds a binding of ID -> . when the ID field is dot in the VCF
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-- Really we should make ID a primary key in VariantContext. Putting it into the attributes is just annoying now
2011-10-18 10:57:02 -04:00
e45fcb66eb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-17 15:56:19 -04:00
1e6794c539
fixing typo in VariantsToTable docs
2011-10-17 15:56:02 -04:00
0de8550f17
Merged bug fix from Stable into Unstable
2011-10-17 15:29:53 -04:00
c1329c4dde
Fixing a binary to logical or
2011-10-17 15:29:45 -04:00
9e4963efc8
Merged bug fix from Stable into Unstable
2011-10-17 15:27:38 -04:00
ec911ce5bb
Even better error messages
2011-10-17 15:27:22 -04:00
d065bf1715
Merged bug fix from Stable into Unstable
2011-10-17 15:25:47 -04:00
a7cf9cdc67
Fixing error message typo
2011-10-17 15:25:35 -04:00
589df6b7cf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-17 14:35:14 -04:00
6b02354d84
Adding a new getter in VariantsToTable to extract the indel event length.
2011-10-17 14:34:52 -04:00
3550798c4c
Merged bug fix from Stable into Unstable
2011-10-17 13:58:56 -04:00
4108a294f7
Better error message when a RodBinding file doesn't exist
2011-10-17 13:58:46 -04:00
cc76826f78
Merged bug fix from Stable into Unstable
2011-10-17 13:38:11 -04:00
fd4540cd32
Fixed extraordinarily subtle race condition with contracts invariant
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-- all of the methods in the class must be synchronized or the internal state can be inconsistent with the contract invariant when entering the class in a non-synchronized method, even when that method doesn't care about the object's internal state
2011-10-17 13:37:55 -04:00
5a881360df
Merged bug fix from Stable into Unstable
2011-10-13 15:54:43 -04:00
7cab6f6bb0
Bug fixes for thread unsafe simple timer and bad Ns treatment in AlignmentUtils
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-- SimpleTimer is now threadsafe using synchronized method keywords
-- Bug fix for alignmentToByteArray() where the N case was refPos++ not the now correct refPos += elementLength
2011-10-13 15:53:12 -04:00
e12ffb6547
Updating docs for GCContentByInterval
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This walker does not take any BAMs. It only walks over the reference.
2011-10-13 13:27:00 -04:00
9aecd50473
Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.
2011-10-12 15:44:54 -04:00
e53a952aeb
Added ION Torrent support to CountCovariates.
2011-10-12 01:57:02 -04:00
a2733a451f
Added NotCalled feature to GAV
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Added "not called" and "no status" to the truth table. Very useful.
2011-10-11 19:31:45 -04:00
ae83420637
Merged bug fix from Stable into Unstable
2011-10-11 12:26:08 -04:00
794f275871
SnpEff is now marked as a RodRequiringAnnotation instead of an ExperimentalAnnotation.
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Having SnpEff grouped with the Experimental annotations was proving problematic, since it
requires a rod. Placing it in its own group should improve the situation somewhat, making it
easier to request "all annotations except for SnpEff".
2011-10-11 12:08:56 -04:00
cfd0ac8410
Merged bug fix from Stable into Unstable
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Conflicts:
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
2011-10-11 12:03:51 -04:00
24b72334b3
UnifiedGenotyper now correctly initializes the VariantAnnotator engine.
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This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
2011-10-11 12:02:05 -04:00
0429b38021
Merged bug fix from Stable into Unstable
2011-10-11 11:19:38 -04:00
1c485d8b5e
Forgot that no matter how trivial a change it's a good idea to compile first
2011-10-11 11:18:41 -04:00
6418f4d69b
Merged bug fix from Stable into Unstable
2011-10-11 11:13:18 -04:00
1975de1b32
Second try: hide --do_indel_quality in AnalyzeCovariates
2011-10-11 11:11:29 -04:00
6506ea83e8
Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through.
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This reverts commit 70e10ccb1be90dcff8f4485ae6ee036db2d1ac86.
2011-10-11 11:03:12 -04:00
4c1d8c8d44
Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users
2011-10-11 11:01:06 -04:00
77c983c5b5
No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public.
2011-10-10 15:17:54 -04:00
Mark DePristo
Christopher Hartl
Eric Banks
Mauricio Carneiro
Ryan Poplin
David Roazen
Guillermo del Angel