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It has options to allow for the conversion of the sequence to/from '=' from/to the actual bases by using the reference sequence.
It has options to allow for the conversion of the sequence to/from '=' from/to the actual bases by using the reference sequence.
It also has an option to left shift indels in the CIGARs before writing the output file.
If you want to convert a BAM file to a SAM file, just call:
If you want to convert a BAM file to a SAM file, just call:
= Usage =
= Usage =
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <reference filename>] [--seqBases|--seqEquals|--seqOrig] [--recover] [--noeof] [--params]
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <reference filename>] [--useBases|--useEquals|--useOrigSeq] [--lshift] [--noeof] [--params]
Optional Parameters:
Optional Parameters:
--refFile : reference file name
--refFile : reference file name
--noeof : do not expect an EOF block on a bam file.
--lshift : left shift indels when writing records
--noeof : do not expect an EOF block on a bam file
--params : print the parameter settings
--params : print the parameter settings
--recover : attempt to recover the input bam file.
--recover : attempt to recover the input bam file
Optional Sequence Parameters (only specify one):
Optional Sequence Parameters (only specify one):
--seqOrig : Leave the sequence as is (default & used if reference is not specified).
--seqOrig : Leave the sequence as is (default & used if reference is not specified)
--seqBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --ref).
--seqBases : Convert any '=' in the sequence to the appropriate base using the reference (requires --ref)
--seqEquals : Convert any bases that match the reference to '=' (requires --ref).
--seqEquals : Convert any bases that match the reference to '=' (requires --ref)
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{{InBAMInputFile}}
{{InBAMInputFile}}
{{OutBAMOutputFile}}
{{refFile}}
== Left Shift Indels in the CIGAR (<code>--lshift</code>) ==
Left shift indels as far as they can go in the read.
{{noeofBGZFParameter}}
{{paramsParameter}}
== Recover a corrupted BAM file (<code>--recover</code>) ==
== Recover a corrupted BAM file (<code>--recover</code>) ==
