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= Overview of the <code>convert</code> function of <code>bamUtil</code> =
The <code>convert</code> option on the bam executable reads a SAM/BAM file and writes it as a SAM/BAM file.
The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, just call:
<pathToExe>/bam --in <bamFile>.bam --out <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
= Sequence Representation =
The sequence parameter options specify how to represent the sequence if the reference is specified (refFile option). If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='.
== Examples ==
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AATAA CTAGA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AATAACTAGATAGGG
Sequence with Bases: AATAACTAGATAGGG
Sequence with Equals: AA======G===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AATGA CTGGA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AATGACTGGATAGGG
Sequence with Bases: AATGACTGGATAGGG
Sequence with Equals: AA=G===GG===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AAT=A CT=GA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AAT=ACT=GATAGGG
Sequence with Bases: AATGACTGGATAGGG
Sequence with Equals: AA======G===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AA=== ===G= = =GGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AA======G===GGG
Sequence with Bases: AATAACTAGATAGGG
Sequence with Equals: AA======G===GGG
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--refFile : reference file name
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
Optional Sequence Parameters (only specify one):
--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).
--seqEquals : Convert any bases that match the reference to '=' (requires --ref).
</pre>
= Usage =
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <reference filename>] [--seqBases|--seqEquals|--seqOrig] [--noeof] [--params]
= Return Value =
Returns the SamStatus for the reads/writes.
= Example Output =
<pre>
Number of records read = 10
Number of records written = 10
</pre>
The <code>convert</code> option on the bam executable reads a SAM/BAM file and writes it as a SAM/BAM file.
The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, just call:
<pathToExe>/bam --in <bamFile>.bam --out <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
= Sequence Representation =
The sequence parameter options specify how to represent the sequence if the reference is specified (refFile option). If the reference is not specified or seqOrig is specified, no modifications are made to the sequence. If the reference and seqBases is specified, any matches between the sequence and the reference are represented in the sequence as the appropriate base. If the reference and seqEquals is specified, any matches between the sequence and the reference are represented in the sequence as '='.
== Examples ==
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AATAA CTAGA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AATAACTAGATAGGG
Sequence with Bases: AATAACTAGATAGGG
Sequence with Equals: AA======G===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AATGA CTGGA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AATGACTGGATAGGG
Sequence with Bases: AATGACTGGATAGGG
Sequence with Equals: AA=G===GG===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AAT=A CT=GA T AGGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AAT=ACT=GATAGGG
Sequence with Bases: AATGACTGGATAGGG
Sequence with Equals: AA======G===GGG
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AA=== ===G= = =GGG
Reference: TAACCCTA ACCCT A
Sequence with Orig: AA======G===GGG
Sequence with Bases: AATAACTAGATAGGG
Sequence with Equals: AA======G===GGG
= Parameters =
<pre>
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--refFile : reference file name
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
Optional Sequence Parameters (only specify one):
--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).
--seqEquals : Convert any bases that match the reference to '=' (requires --ref).
</pre>
= Usage =
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--refFile <reference filename>] [--seqBases|--seqEquals|--seqOrig] [--noeof] [--params]
= Return Value =
Returns the SamStatus for the reads/writes.
= Example Output =
<pre>
Number of records read = 10
Number of records written = 10
</pre>
