3 Merges alignment data from a SAM or BAM file with additional data stored in an unmapped BAM file and produces a third SAM or BAM file of aligned and unaligned reads. NOTE that this program expects to find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it to have the same base name as the reference fasta except with the extension '.dict'
109 <param name="title" label="Name for the output merged BAM or SAM file" type="text" default="Merged.bam" help="This name will appear in your history so use it to remember what the new file in your history contains" />
114 <param name="UNMAPPED_BAM" label="Original SAM or BAM file of unmapped reads, which must be in queryname order. Required." type="data" format="bam,sam" />
118 <param name="ALIGNED_BAM" label="SAM or BAM file(s) with alignment data. This option may be specified 0 or more times. Cannot be used in conjuction with option(s) READ1_ALIGNED_BAM (R1_ALIGNED) READ2_ALIGNED_BAM (R2_ALIGNED)" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
122 <param name="READ1_ALIGNED_BAM" label="SAM or BAM file(s) with alignment data from the first read of a pair. This option may be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM (ALIGNED)" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
126 <param name="READ2_ALIGNED_BAM" label="SAM or BAM file(s) with alignment data from the second read of a pair. This option may be specified 0 or more times. Cannot be used in conjuction with option(s) ALIGNED_BAM (ALIGNED)" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
132 <param name="PROGRAM_GROUP_COMMAND_LINE" label="The command line of the program group (if not supplied by the aligned file)." type="text" default="" />
135 <param name="IS_BISULFITE_SEQUENCE" value="false" type="boolean" label="Whether the lane is bisulfite sequence (used when caculating the NM tag)." truevalue="true" falsevalue="false" checked="yes" />
139 help="Alignments with more than this many insertions or deletions will be ignored. Set to -1 to allow any number of insertions or deletions. Default value: 1." />
141 <param name="ATTRIBUTES_TO_RETAIN" label="Reserved alignment attributes (tags starting with X, Y, or Z) that should be brought over from the alignment data when merging. This option may be specified 0 or more times." type="text" default="" />
158 <param name="PRIMARY_ALIGNMENT_STRATEGY" label="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." type="select" help="BestMapq expects that multiple alignments will be correlated with HI tag, and prefers the pair of
159 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. Default value: BestMapq.">
166 <param name="CLIP_OVERLAPPING_READS" value="true" type="boolean" label="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." truevalue="true" falsevalue="false" checked="yes" />
191 Merges alignment data from a SAM or BAM file with additional data stored in an unmapped BAM file and produces a third SAM or BAM file of aligned and unaligned reads. NOTE that this program expects to find a sequence dictionary in the same directory as REFERENCE_SEQUENCE and expects it to have the same base name as the reference fasta except with the extension '.dict'