New upstream version 1.2.14 (72ba2085) · Commits · Debian Med / paleomix

CHANGES.md

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		# Changelog

		## [1.2.14] - 2019-12-01
		### Changed
		- Improved handling of K-groups in zonkey database files
		- Change BAM pipeline version requirement for GATK to < v4.0, as the
		the Indel Realigner has been removed in GATK v4.0

		### Fixed
		- Fixed version detection of GATK for v4.0 (issue #23)


		## [1.2.13.8] - 2019-10-27
		### Changed
		- Zonkey now identifies nuclear chromosomes by size instead of name; this
		is done to better handle FASTAs downloaded from different sources


		## [1.2.13.7] - 2019-10-15
		### Fixed
		- Fixed handling of digit only chromosome names in Zonkey
		- Remove dashes from Zonkey MT genomes when running 'mito' command


		## [1.2.13.6] - 2019-10-13
		### Fixed
		- Handle .*miss files created by some versions of plink in Zonkey


		## [1.2.13.5] - 2019-09-29
		### Fixed
		- Ignore ValidateSamFile warning REF_SEQ_TOO_LONG_FOR_BAI warning when
		processing genomes with contigs too large for BAI index files.


		## [1.2.13.4] - 2019-03-25
		### Fixed
		- Improved detection of Picard versions in cases where 'java'
		@@ -587,7 +620,12 @@ the (partially) updated documentation now hosted on ReadTheDocs.
		- Switching to more traditional version-number tracking.


		[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...HEAD
		[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.14...HEAD
		[1.2.14]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.8...v1.2.14
		[1.2.13.8]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.7...v1.2.13.8
		[1.2.13.7]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.6...v1.2.13.7
		[1.2.13.6]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.5...v1.2.13.6
		[1.2.13.5]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...v1.2.13.5
		[1.2.13.4]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...v1.2.13.4
		[1.2.13.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3
		[1.2.13.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2

docs/conf.py

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		@@ -57,7 +57,7 @@ author = u'Mikkel Schubert'
		# The short X.Y version.
		version = u'1.2'
		# The full version, including alpha/beta/rc tags.
		release = u'1.2.13'
		release = u'1.2.14'

		# The language for content autogenerated by Sphinx. Refer to documentation
		# for a list of supported languages.

paleomix/init.py

+2 −2

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		@@ -21,8 +21,8 @@
		# SOFTWARE.
		#

		__version_info__ = (1, 2, 13, 3)
		__version__ = '%i.%i.%i.%i' % __version_info__
		__version_info__ = (1, 2, 14)
		__version__ = "%i.%i.%i" % __version_info__


		def run(command=None):

paleomix/nodes/gatk.py

+5 −2

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		@@ -45,6 +45,9 @@ from paleomix.nodes.bwa import \
		import paleomix.common.versions as versions


		_RE_GATK_VERSION = r"^(?:The Genome Analysis Toolkit \(GATK\) v)?(\d+)\.(\d+)"


		def _get_gatk_version_check(config):
		"""Returns a version-check object for the "GenomeAnalysisTK.jar" located at
		config.jar_root; for now, this check only serves to verify that the JAR can
		@@ -60,8 +63,8 @@ def _get_gatk_version_check(config):
		# Any version is fine; for now just catch old JREs
		requirement = versions.Requirement(call=params.finalized_call,
		name="GenomeAnalysisTK",
		search=r"^(\d+)\.(\d+)",
		checks=versions.Any())
		search=_RE_GATK_VERSION,
		checks=versions.LT(4, 0))
		_GATK_VERSION[jar_file] = requirement
		return _GATK_VERSION[jar_file]
		_GATK_VERSION = {}

paleomix/nodes/picard.py

+22 −2

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		@@ -60,10 +60,13 @@ class PicardNode(CommandNode):

		class ValidateBAMNode(PicardNode):
		def __init__(self, config, input_bam, input_index=None, output_log=None,
		ignored_checks=(), dependencies=()):
		ignored_checks=(), big_genome_mode=False, dependencies=()):
		builder = picard_command(config, "ValidateSamFile")
		_set_max_open_files(builder, "MAX_OPEN_TEMP_FILES")

		if True or big_genome_mode:
		self._configure_for_big_genome(config, builder)

		builder.set_option("I", "%(IN_BAM)s", sep="=")
		for check in ignored_checks:
		builder.add_option("IGNORE", check, sep="=")
		@@ -79,6 +82,22 @@ class ValidateBAMNode(PicardNode):
		description=description,
		dependencies=dependencies)

		@staticmethod
		def _configure_for_big_genome(config, builder):
		# CSI uses a different method for assigning BINs to records, which
		# Picard currently does not support.
		builder.add_option("IGNORE", "INVALID_INDEXING_BIN", sep="=")

		jar_path = os.path.join(config.jar_root, _PICARD_JAR)
		version_check = _PICARD_VERSION_CACHE[jar_path]

		try:
		if version_check.version >= (2, 19, 0):
		# Useless warning, as we do not build BAI indexes for large genomes
		builder.add_option("IGNORE", "REF_SEQ_TOO_LONG_FOR_BAI", sep="=")
		except versions.VersionRequirementError:
		pass # Ignored here, handled elsewhere


		class BuildSequenceDictNode(PicardNode):
		def __init__(self, config, reference, dependencies=()):
		@@ -247,7 +266,8 @@ def picard_command(config, command):
		params = AtomicJavaCmdBuilder(jar_path,
		temp_root=config.temp_root,
		jre_options=config.jre_options,
		CHECK_JAR=version)
		CHECK_JAR=version,
		set_cwd=True)
		params.set_option(command)

		return params