- Updated the documentation on the code
- Made the table.write() method private and updated necessary files.
- Added a constructor to GATKReport that takes GATKReportTables
- Optimized my code
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
This is important for quick turnaround in the analysis cycle of the new covariates. Also added a dummy unit test that doesn't really test anything (disabled), but helps in debugging.
Pulled out the functionality from Indel Realigner and Table Recalibrator into Utils.setupWriter to make everyone else's life's easier if they want to include the PG tag in their walkers.
Infrastructure:
* Added static interface to all different clipping algorithms of low quality tail clipping
* Added reverse direction pileup element event lookup (indels) to the PileupElement and LocusIteratorByState
* Complete refactor of the KeyManager. Much cleaner implementation that handles keys with no optional covariates (necessary for on-the-fly recalibration)
* EventType is now an independent enum with added capabilities. All functionality is now centralized.
BQSR and RecalibrateBases:
* On-the-fly recalibration is now generic and uses the same bit set structure as BQSR for a reduced memory footprint
* Refactored the object creation to take advantage of the compact key structure
* Replaced nested hash maps with single hash maps indexed by bitsets
* Eliminated low quality tails from the context covariate (using ReadClipper's write N's algorithm).
* Excluded contexts with N's from the output file.
* Fixed cycle covariate for discrete platforms (need to check flow cycle platforms now!)
* Redfined error for indels to look at the previous base in negative strand reads (using new PE functionality)
* Added the covariate ID (for optional covariates) to the output for disambiguation purposes
* Refactored CovariateKeySet -- eventType functionality is now handled by the EventType enum.
* Reduced memory usage of the BQSR script to 4
Tests:
* Refactored BQSRKeyManagerUnitTest to handle the new implementation of the key manager
* Added tests for keys without optional covariates
* Added tests for on-the-fly recalibration (but more tests are necessary)
Infrastructure:
* Generic BitSet implementation with any precision (up to long)
* Two's complement implementation of the bit set handles negative numbers (cycle covariate)
* Memoized implementation of the BitSet utils for better performance.
* All exponents are now calculated with bit shifts, fixing numerical precision issues with the double Math.pow.
* Replace log/sqrt with bitwise logic to get rid of numerical issues
BQSR:
* All covariates output BitSets and have the functionality to decode them back into Object values.
* Covariates are responsible for determining the size of the key they will use (number of bits).
* Generalized KeyManager implementation combines any arbitrary number of covariates into one bitset key with event type
* No more NestedHashMaps. Single key system now fits in one hash to reduce hash table objects overhead
Tests:
* Unit tests added to every method of BitSetUtils
* Unit tests added to the generalized key system infrastructure of BQSRv2 (KeyManager)
* Unit tests added to the cycle and context covariates (will add unit tests to all covariates)
-- TODO for ryan -- there are bugs in ActivityProfile code that I cannot fix right now :-(
-- UnitTesting framework for ActivityProfile -- needs to be expanded
-- Minor helper functions for ActiveRegion to help with unit tests
-- Refactored ART into clearer, simpler procedures. Attempted to merge shared code into utility classes.
-- Added some docs
-- Created a new, testable ActivityProfile that represents as a class the probability of a base being active or inactive
-- Separated band-pass filtering from creation of active regions. Now you can band pass filter a profile to make another profile, and then that is explicitly converted to active regions
-- Misc. utility functions in ActiveRegionWalker such as hasPresetActiveRegions()
-- Many TODOs in ActivityProfile.
-- This report details which intervals are coming in and how many reads they contain
-- Added integration test to verify that the intervals aren't changing, before heading into the ART refactor
GATKReport format changes:
- All non-data header lines are preceeded with a single pound ( #:)
- Every report now has a report header containing the version number and number of tables
- Every table has two lines of table header: The first explains the size of the table and the data types of each column, the second contains the table name and description.
- This new format will allow reports in the future to be gatherable.
- Changed the header format to include an end-of-line string ":;"
Added features:
- Simplified GATK Reports:
The constructor for a simplified GATK Report. Simplified GATK report are designed for reports that do not need the advanced functionality of a full GATK Report.
A simple GATK Report consists of:
- A single table
- No primary key ( it is hidden )
Optional:
- Only untyped columns. As long as the data is an Object, it will be accepted.
- Default column values being empty strings.
Limitations:
- A simple GATK report cannot contain multiple tables.
- It cannot contain typed columns, which prevents arithmetic gathering.
- Added a constructor to generate simplified GATK reports.
- Added a method to easily add data to simple GATK reports.
- Upgraded the input parser take advantage of the new file format (v1).
- Added the GATKReportGatherer, more usability cmoing in next versionof GATK Report. Curently, it can only add rows from one table to another. Added private methods in GATKReport to combine Tables and Reports, It is very conservative and will only gather if the table columns, as well as everything else matches. At the column level, it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data.
- Made some GATKReport methods public, and added more setters and getters.
- Added method that compares formats of two GATKReports, and added an equals method to verify all data inside.
- The gsalib for R now supports reading GATKReport v1 files in addition to legacy formats (v0.*)
- Added a GATKReportDataType enum to give column a certain data type. This must be specified when making a gatherable report. This enum contains several methods including a reverse lookup map.
- Added a data type field in GATKColumn, when a type is not specified, the unknown type is used. Unknown types should not be gathered.
Test changes:
- Updated Unit Tests for GATK Report v1. Added a test for the gatherer. Left one test disabled while we transition from v0 to v1.
- Updated the MD5 hashes in integration tests throughout the GATK.
Other changes:
- Added the gatherer functions to CoverageByRG
- Also added the scatterCount parameter in the Interval Coverage script
- Dropped support for reading in legacy GATKReport formats ( v0.*)
- Updated VariantEvalWalker to work with GATK Report v1, added a format String to all applicable DataPoints.
- Rewrote the read file method for GATK report files.
- Optimized the equals methods within GATKReport. The protected functions should only be called by the GATKReport methods.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Now looks like:
<GATK-run-report>
<id>D7D31ULwTSxlAwnEOSmW6Z4PawXwMxEz</id>
<start-time>2012/03/10 20.21.19</start-time>
<end-time>2012/03/10 20.21.19</end-time>
<run-time>0</run-time>
<walker-name>CountReads</walker-name>
<svn-version>1.4-483-g63ecdb2</svn-version>
<total-memory>85000192</total-memory>
<max-memory>129957888</max-memory>
<user-name>depristo</user-name>
<host-name>10.0.1.10</host-name>
<java>Apple Inc.-1.6.0_26</java>
<machine>Mac OS X-x86_64</machine>
<iterations>105</iterations>
</GATK-run-report>
No longer capturing command line or directory information, to minimize people's concerns with phone home and privacy
-- Refactored some duplicated code (FYI, code duplication = root of all evil) into shared functions
-- Added long-missing integrationtests
-- CHRIS/RYAN -- it would be very good to add an integration test covering external VCF files as I believe we rely on this functionality and it's not tested at all
This is a quick-and-dirty patch for the null pointer error Mauricio reported earlier.
Later on we might want to address in a more general way the fact that we validate user intervals
against the reference but not against the merged BAM header produced by the engine at runtime.
This fix is similar, but distinct from the earlier fix to GATKBAMIndex. If we fail to read in
a complete 3-integer bin header from the BAM schedule file that the engine has written, throw a
ReviewedStingException (since this is our problem, not the user's) rather than allowing a
cryptic buffer underflow error to occur.
Note that this change does not fix the underlying problem in the engine, if there is one
(there may be an as-yet-undetected bug in the code that writes the bam schedule). It will
just make it easier for us to identify what's going wrong in the future.
GATKBAMIndex would allow an extremely confusing BufferUnderflowException to be
thrown when a BAM index file was truncated or corrupt. Now, a UserException is
thrown in this situation instructing the user to re-index the BAM.
Added a unit test for this case as well.
-- A cleaner table output (molten). For those interested in seeing how this can be done with GATKReports look here for a nice clean example
-- Integration tests
-- Minor improvements to GATKReportTable with methods to getPrimaryKeys
-- We weren't properly handling the case where a site had both a SNP and indel in both eval and comp. These would naturally pair off as SNP x SNP and INDEL x INDEL in eval, but we'd still invoke update2 with (null, SNP) and (null, INDEL) resulting most conspicously as incorrect false negatives in the validation report.
-- Updating misc. integrationtests, as the counting of comps (in particular for dbSNP) was inflated because of this effect.
Several of the unit tests for the new key authorization feature require
read access to the GATK master private key file. Since this file is only
readable by members of the group gsagit, this makes it hard for people
outside the group to run the test suite.
Now, we skip tests that require the master private key if the private
key exists (since not existing would be a true error) but is not readable
by the user running the test suite
Bamboo, of course, will always be able to run these tests.
-Running the GATK with the -et NO_ET or -et STDOUT options now
requires a key issued by us. Our reasons for doing this, and the
procedure for our users to request keys, are documented here:
http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home
-A GATK user key is an email address plus a cryptographic signature
signed using our private key, all wrapped in a GZIP container.
User keys are validated using the public key we now distribute with
the GATK. Our private key is kept in a secure location.
-Keys are cryptographically secure in that valid keys definitely
came from us and keys cannot be fabricated, however keys are not
"copy-protected" in any way.
-Includes private, standalone utilities to create a new GATK user key
(GenerateGATKUserKey) and to create a new master public/private key
pair (GenerateKeyPair). Usage of these tools will be documented on
the internal wiki shortly.
-Comprehensive unit/integration tests, including tests to ensure the
continued integrity of the GATK master public/private key pair.
-Generation of new user keys and the new unit/integration tests both
require access to the GATK private key, which can only be read by
members of the group "gsagit".
-- Includes paired end status (T/F)
-- Includes count of reads used in calculation
-- Includes simple read type (2x76 for example)
-- Better handling of insert size, read length when there's no data, or the data isn't paired end by emitting NA not 0
-- ReadGroupProperties: Emits a GATKReport containing read group, sample, library, platform, center, median insert size and median read length for each read group in every BAM file.
-- Median tool that collects up to a given maximum number of elements and returns the median of the elements.
-- Unit and integration tests for everything.
-- Making name of TestProvider protected so subclasses and override name more easily
* All contexts with 'N' bases are now collapsed as uninformative
* Context size is now represented internally as a BitSet but output as a dna string
* Temporarily disabled sorted outputs because of null objects
* Turns DNA sequences (for context covariates) into bit sets for maximum compression
* Allows variable context size representation guaranteeing uniqueness.
* Works with long precision, so it is limited to a context size of 31 bases (can be extended with BigNumber precision if necessary).
* Unit Tests added
-- As these represent the bulk of the StingExceptions coming from BAMSchedule and are caused by simple problems like the user providing bad input tmp directories, etc.
-- DoC now by default ignores bases with reference Ns, so these are not included in the coverage calculations at any stage.
-- Added option --includeRefNSites that will include them in the calculation
-- Added integration tests that ensures the per base tables (and so all subsequent calculations) work with and without reference N bases included
-- Reorganized command line options, tagging advanced options with @Advanced
* The tailSet generated every time we flush the reads stash is still being affected by subsequent clears because it is just a pointer to the parent element in the original TreeSet. This is dangerous, and there is a weird condition where the clear will affects it.
* Fix by creating a new set, given the tailSet instead of trying to do magic with just the pointer.
When aggregating raw BAM file spans into shards, the IntervalSharder tries to combine
file spans when it can. Unfortunately, the method that combines two BAM file
spans was seriously flawed, and would produce a truncated union if the file spans
overlapped in certain ways. This could cause entire regions of the BAM file containing
reads within the requested intervals to be dropped.
Modified GATKBAMFileSpan.union() to correct this problem, and added unit tests
to verify that the correct union is produced regardless of how the file spans
happen to overlap.
Thanks to Khalid, who did at least as much work on this bug as I did.
so Ryan can work on the recalibration on the fly without breaking the build. Supposedly all the secret sauce is in the BQSR walker, which sits in private.
* added support to base before deletion in the pileup
* refactored covariates to operate on mismatches, insertions and deletions at the same time
* all code is in private so original BQSR is still working as usual in public
* outputs a molten CSV with mismatches, insertions and deletions, time to play!
* barely tested, passes my very simple tests... haven't tested edge cases.
premature push from my part. Roger is still working on the new format and we need to update the other tools to operate correctly with the new GATKReport.
This reverts commit aea0de314220810c2666055dc75f04f9010436ad.
- Added the GATKReportGatherer
- Added private methods in GATKReport to combine Tables and Reports
- It is very conservative and it will only gather if the table columns, match.
- At the column level it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data.
Added the gatherer functions to CoverageByRG
Also added the scatterCount parameter in the Interval Coverage script
Made some more GATKReport methods public
The UnitTest included shows that the merging methods work
Added a getter for the PrimaryKeyName
Fixed bugs that prevented the gatherer form working
Working GATKReportGatherer
Has only the functional to addLines
The input file parser assumes that the first column is the primary key
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
* Adding the context covariate standard in both modes (including old CountCovariates) with parameters
* Updating all covariates and modules to use GATKSAMRecord throughout the code.
* BQSR now processes indels in the pileup (but doesn't do anything with them yet)
* calculates and interprets the coverage of a given interval track
* allows to expand intervals by specified number of bases
* classifies targets as CALLABLE, LOW_COVERAGE, EXCESSIVE_COVERAGE and POOR_QUALITY.
* outputs text file for now (testing purposes only), soon to be VCF.
* filters are overly aggressive for now.
Roger Zurawicki
Mauricio Carneiro
Ryan Poplin
Eric Banks
Guillermo del Angel
Mark DePristo
David Roazen
Andrey Sivachenko
Christopher Hartl
Lechu
Khalid Shakir
Matt Hanna