def get_gatk_jar_version(name, fname): if name == "gatk": return broad.get_gatk_version(fname) elif name == "mutect": return broad.get_mutect_version(fname) else: raise ValueError("Unexpected GATK input: %s" % name)
def includes_missingalt(data): """ As of GATK 4.1.0.0, variants with missing alts are generated (see https://github.com/broadinstitute/gatk/issues/5650) """ MISSINGALT_VERSION = LooseVersion("4.1.0.0") version = LooseVersion(broad.get_gatk_version(config=dd.get_config(data))) return version >= MISSINGALT_VERSION
def includes_missingalt(data): """ As of GATK 4.1.0.0, variants with missing alts are generated (see https://github.com/broadinstitute/gatk/issues/5650) """ MISSINGALT_VERSION = LooseVersion("4.1.0.0") version = LooseVersion(broad.get_gatk_version(config=dd.get_config(data))) try: return version >= MISSINGALT_VERSION except TypeError: logger.error( f"LooseVersion failing with {version} as the detected version.") sys.exit(1)
def _install_gatk_jar(name, fname, manifest, system_config, toolplus_dir): """Install a jar for GATK or associated tools like MuTect. """ if not fname.endswith(".jar"): raise ValueError("--toolplus argument for %s expects a jar file: %s" % (name, fname)) if name == "gatk": version = broad.get_gatk_version(fname) elif name == "mutect": version = broad.get_mutect_version(fname) else: raise ValueError("Unexpected GATK input: %s" % name) store_dir = utils.safe_makedir(os.path.join(toolplus_dir, name, version)) shutil.copyfile(fname, os.path.join(store_dir, os.path.basename(fname))) _update_system_file(system_config, name, {"dir": store_dir}) _update_manifest(manifest, name, version)