def __init__(self, config, input_bams, pipename="input.bam"):
self.pipe = pipename
self.files = safe_coerce_to_tuple(input_bams)
self.commands = []
self.kwargs = {"TEMP_IN_BAM": self.pipe}
if len(self.files) > 1:
jar_file = os.path.join(config.jar_root, "MergeSamFiles.jar")
params = AtomicJavaCmdBuilder(jar=jar_file,
temp_root=config.temp_root,
jre_options=config.jre_options)
params.set_option("SO", "coordinate", sep="=", fixed=False)
params.set_option("CREATE_INDEX", "False", sep="=")
params.set_option("COMPRESSION_LEVEL", 0, sep="=")
params.set_option("OUTPUT", "%(TEMP_OUT_BAM)s", sep="=")
params.add_multiple_options("I", input_bams, sep="=")
params.set_kwargs(CHECK_JAR=_picard_version(config, jar_file),
TEMP_OUT_BAM=self.pipe)
self.commands = [params.finalize()]
else:
# Ensure that the actual command depends on the input
self.kwargs["IN_FILE_00"] = self.files[0]
self.kwargs["IN_FILE_01"] = swap_ext(self.files[0], ".bai")
def customize(cls, config, input_bams, output_bam, output_metrics=None,
keep_dupes=False, dependencies=()):
jar_file = os.path.join(config.jar_root, "MarkDuplicates.jar")
params = AtomicJavaCmdBuilder(jar_file, jre_options=config.jre_options)
# Create .bai index, since it is required by a lot of other programs
params.set_option("CREATE_INDEX", "True", sep="=")
params.set_option("OUTPUT", "%(OUT_BAM)s", sep="=")
params.set_option("METRICS_FILE", "%(OUT_METRICS)s", sep="=")
params.add_multiple_options("I", input_bams, sep="=")
if not keep_dupes:
# Remove duplicates from output by default to save disk-space
params.set_option("REMOVE_DUPLICATES", "True",
sep="=", fixed=False)
output_metrics = output_metrics or swap_ext(output_bam, ".metrics")
params.set_kwargs(OUT_BAM=output_bam,
OUT_BAI=swap_ext(output_bam, ".bai"),
OUT_METRICS=output_metrics,
CHECK_JAR=_picard_version(config, jar_file))
return {"command": params,
"dependencies": dependencies}
def __init__(self, config, input_bams, pipename="input.bam"):
self.pipe = pipename
self.files = safe_coerce_to_tuple(input_bams)
self.commands = []
self.kwargs = {"TEMP_IN_BAM": self.pipe}
if len(self.files) > 1:
jar_file = os.path.join(config.jar_root, "MergeSamFiles.jar")
params = AtomicJavaCmdBuilder(jar=jar_file,
temp_root=config.temp_root,
jre_options=config.jre_options)
params.set_option("SO", "coordinate", sep="=", fixed=False)
params.set_option("CREATE_INDEX", "False", sep="=")
params.set_option("COMPRESSION_LEVEL", 0, sep="=")
params.set_option("OUTPUT", "%(TEMP_OUT_BAM)s", sep="=")
params.add_multiple_options("I", input_bams, sep="=")
params.set_kwargs(CHECK_JAR=_picard_version(config, jar_file),
TEMP_OUT_BAM=self.pipe)
self.commands = [params.finalize()]
else:
# Ensure that the actual command depends on the input
self.kwargs["IN_FILE_00"] = self.files[0]
self.kwargs["IN_FILE_01"] = swap_ext(self.files[0], ".bai")
def customize(cls,
config,
input_bams,
output_bam,
output_metrics=None,
keep_dupes=False,
dependencies=()):
jar_file = os.path.join(config.jar_root, "MarkDuplicates.jar")
params = AtomicJavaCmdBuilder(jar_file, jre_options=config.jre_options)
# Create .bai index, since it is required by a lot of other programs
params.set_option("CREATE_INDEX", "True", sep="=")
params.set_option("OUTPUT", "%(OUT_BAM)s", sep="=")
params.set_option("METRICS_FILE", "%(OUT_METRICS)s", sep="=")
params.add_multiple_options("I", input_bams, sep="=")
if not keep_dupes:
# Remove duplicates from output by default to save disk-space
params.set_option("REMOVE_DUPLICATES",
"True",
sep="=",
fixed=False)
output_metrics = output_metrics or swap_ext(output_bam, ".metrics")
params.set_kwargs(OUT_BAM=output_bam,
OUT_BAI=swap_ext(output_bam, ".bai"),
OUT_METRICS=output_metrics,
CHECK_JAR=_picard_version(config, jar_file))
return {"command": params, "dependencies": dependencies}
def customize(cls, config, input_bams, output_bam, dependencies=()):
jar_file = os.path.join(config.jar_root, "MergeSamFiles.jar")
params = AtomicJavaCmdBuilder(jar_file, jre_options=config.jre_options)
params.set_option("OUTPUT", "%(OUT_BAM)s", sep="=")
params.set_option("CREATE_INDEX", "True", sep="=")
params.set_option("SO", "coordinate", sep="=", fixed=False)
params.add_multiple_options("I", input_bams, sep="=")
params.set_kwargs(OUT_BAM=output_bam,
OUT_BAI=swap_ext(output_bam, ".bai"),
CHECK_JAR=_picard_version(config, jar_file))
return {"command": params, "dependencies": dependencies}
def customize(cls, config, input_bams, output_bam, dependencies=()):
jar_file = os.path.join(config.jar_root, "MergeSamFiles.jar")
params = AtomicJavaCmdBuilder(jar_file, jre_options=config.jre_options)
params.set_option("OUTPUT", "%(OUT_BAM)s", sep="=")
params.set_option("CREATE_INDEX", "True", sep="=")
params.set_option("SO", "coordinate", sep="=", fixed=False)
params.add_multiple_options("I", input_bams, sep="=")
params.set_kwargs(OUT_BAM=output_bam,
OUT_BAI=swap_ext(output_bam, ".bai"),
CHECK_JAR=_picard_version(config, jar_file))
return {"command": params,
"dependencies": dependencies}
