public class MergeBamAlignment extends CommandLineProgram
Modifier and Type | Field and Description |
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java.lang.Boolean |
ADD_MATE_CIGAR |
java.util.List<java.io.File> |
ALIGNED_BAM |
boolean |
ALIGNED_READS_ONLY |
boolean |
ALIGNER_PROPER_PAIR_FLAGS |
java.util.List<java.lang.String> |
ATTRIBUTES_TO_REMOVE |
java.util.List<java.lang.String> |
ATTRIBUTES_TO_RETAIN |
boolean |
CLIP_ADAPTERS |
boolean |
CLIP_OVERLAPPING_READS |
java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> |
EXPECTED_ORIENTATIONS |
boolean |
INCLUDE_SECONDARY_ALIGNMENTS |
boolean |
IS_BISULFITE_SEQUENCE |
java.lang.Integer |
JUMP_SIZE |
int |
MAX_INSERTIONS_OR_DELETIONS |
int |
MIN_UNCLIPPED_BASES |
java.io.File |
OUTPUT |
java.lang.Boolean |
PAIRED_RUN
Deprecated.
|
picard.sam.MergeBamAlignment.PrimaryAlignmentStrategy |
PRIMARY_ALIGNMENT_STRATEGY |
java.lang.String |
PROGRAM_GROUP_COMMAND_LINE |
java.lang.String |
PROGRAM_GROUP_NAME |
java.lang.String |
PROGRAM_GROUP_VERSION |
java.lang.String |
PROGRAM_RECORD_ID |
java.util.List<java.io.File> |
READ1_ALIGNED_BAM |
int |
READ1_TRIM |
java.util.List<java.io.File> |
READ2_ALIGNED_BAM |
int |
READ2_TRIM |
java.io.File |
REFERENCE_SEQUENCE |
htsjdk.samtools.SAMFileHeader.SortOrder |
SORT_ORDER |
boolean |
UNMAP_CONTAMINANT_READS |
java.io.File |
UNMAPPED_BAM |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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MergeBamAlignment() |
Modifier and Type | Method and Description |
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protected java.lang.String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
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protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] argv)
Required main method implementation.
|
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="UNMAPPED", doc="Original SAM or BAM file of unmapped reads, which must be in queryname order.") public java.io.File UNMAPPED_BAM
@Option(shortName="ALIGNED", doc="SAM or BAM file(s) with alignment data.", mutex={"READ1_ALIGNED_BAM","READ2_ALIGNED_BAM"}, optional=true) public java.util.List<java.io.File> ALIGNED_BAM
@Option(shortName="R1_ALIGNED", doc="SAM or BAM file(s) with alignment data from the first read of a pair.", mutex="ALIGNED_BAM", optional=true) public java.util.List<java.io.File> READ1_ALIGNED_BAM
@Option(shortName="R2_ALIGNED", doc="SAM or BAM file(s) with alignment data from the second read of a pair.", mutex="ALIGNED_BAM", optional=true) public java.util.List<java.io.File> READ2_ALIGNED_BAM
@Option(shortName="R", doc="Path to the fasta file for the reference sequence.") public java.io.File REFERENCE_SEQUENCE
@Option(shortName="PG", doc="The program group ID of the aligner (if not supplied by the aligned file).", optional=true) public java.lang.String PROGRAM_RECORD_ID
@Option(shortName="PG_VERSION", doc="The version of the program group (if not supplied by the aligned file).", optional=true) public java.lang.String PROGRAM_GROUP_VERSION
@Option(shortName="PG_COMMAND", doc="The command line of the program group (if not supplied by the aligned file).", optional=true) public java.lang.String PROGRAM_GROUP_COMMAND_LINE
@Option(shortName="PG_NAME", doc="The name of the program group (if not supplied by the aligned file).", optional=true) public java.lang.String PROGRAM_GROUP_NAME
@Deprecated @Option(doc="This argument is ignored and will be removed.", shortName="PE", optional=true) public java.lang.Boolean PAIRED_RUN
@Option(doc="The expected jump size (required if this is a jumping library). Deprecated. Use EXPECTED_ORIENTATIONS instead", shortName="JUMP", mutex="EXPECTED_ORIENTATIONS", optional=true) public java.lang.Integer JUMP_SIZE
@Option(doc="Whether to clip adapters where identified.") public boolean CLIP_ADAPTERS
@Option(doc="Whether the lane is bisulfite sequence (used when caculating the NM tag).") public boolean IS_BISULFITE_SEQUENCE
@Option(doc="Whether to output only aligned reads. ") public boolean ALIGNED_READS_ONLY
@Option(doc="The maximum number of insertions or deletions permitted for an alignment to be included. Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions.", shortName="MAX_GAPS") public int MAX_INSERTIONS_OR_DELETIONS
@Option(doc="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging.") public java.util.List<java.lang.String> ATTRIBUTES_TO_RETAIN
@Option(doc="Attributes from the alignment record that should be removed when merging. This overrides ATTRIBUTES_TO_RETAIN if they share common tags.") public java.util.List<java.lang.String> ATTRIBUTES_TO_REMOVE
@Option(shortName="R1_TRIM", doc="The number of bases trimmed from the beginning of read 1 prior to alignment") public int READ1_TRIM
@Option(shortName="R2_TRIM", doc="The number of bases trimmed from the beginning of read 2 prior to alignment") public int READ2_TRIM
@Option(shortName="ORIENTATIONS", doc="The expected orientation of proper read pairs. Replaces JUMP_SIZE", mutex="JUMP_SIZE", optional=true) public java.util.List<htsjdk.samtools.SamPairUtil.PairOrientation> EXPECTED_ORIENTATIONS
@Option(doc="Use the aligner\'s idea of what a proper pair is rather than computing in this program.") public boolean ALIGNER_PROPER_PAIR_FLAGS
@Option(shortName="SO", doc="The order in which the merged reads should be output.") public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER
@Option(doc="Strategy for selecting primary alignment when the aligner has provided more than one alignment for a pair or fragment, and none are marked as primary, more than one is marked as primary, or the primary alignment is filtered out for some reason. BestMapq expects that multiple alignments will be correlated with HI tag, and prefers the pair of alignments with the largest MAPQ, in the absence of a primary selected by the aligner. EarliestFragment prefers the alignment which maps the earliest base in the read. Note that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for cases in which the aligner is not pair-aware, and does not output the HI tag. It simply picks the alignment for each end with the highest MAPQ, and makes those alignments primary, regardless of whether the two alignments make sense together.MostDistant is also for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. If all alignments would be chimeric, it picks the alignments for each end with the best MAPQ. For all algorithms, ties are resolved arbitrarily.") public picard.sam.MergeBamAlignment.PrimaryAlignmentStrategy PRIMARY_ALIGNMENT_STRATEGY
@Option(doc="For paired reads, soft clip the 3\' end of each read if necessary so that it does not extend past the 5\' end of its mate.") public boolean CLIP_OVERLAPPING_READS
@Option(doc="If false, do not write secondary alignments to output.") public boolean INCLUDE_SECONDARY_ALIGNMENTS
@Option(shortName="MC", optional=true, doc="Adds the mate CIGAR tag (MC) if true, does not if false.") public java.lang.Boolean ADD_MATE_CIGAR
@Option(shortName="UNMAP_CONTAM", optional=true, doc="Detect reads originating from foreign organisms (e.g. bacterial DNA in a non-bacterial sample),and unmap + label those reads accordingly.") public boolean UNMAP_CONTAMINANT_READS
public static void main(java.lang.String[] argv)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
protected java.lang.String[] customCommandLineValidation()
customCommandLineValidation
in class CommandLineProgram