-- This behavior, which isn't obviously valuable at all, continued to grab and rethrow exceptions in the HMS that, if run without NT, would show up as more meaningful errors. Now HMS simply checks whether the throwable it received on error was a RuntimeException. If so, it is stored and rethrow without wrapping later. If it isn't, only in this case is the exception wrapped in a ReviewedStingException.
-- Added a QC walker ErrorThrowingWalker that will throw a UserException, ReviewedStingException, and NullPointerException from map as specified on the command line
-- Added IT that ensures that all three types are thrown properly (i.e., you catch a NullPointerException when you ask for one to be thrown) with and without threading enabled.
-- I believe this will finally put to rest all of these annoying HMS captures.
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".
Mark DePristo
Ryan Poplin
Guillermo del Angel
Eric Banks
David Roazen
Andrey Sivachenko
Christopher Hartl
Lechu
Mauricio Carneiro