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Don't forget to put in the paths to the executable and your test files.
Don't forget to put in the paths to the executable and your test files.
= Sequence Representation =
= 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>
== Examples ==
== Sequence Representation Parameters ==
The sequence parameters 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
ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS
Sequence: AATAA CTAGA T AGGG
Sequence: AATAA CTAGA T AGGG
Sequence with Equals: AA======G===GGG
Sequence with Equals: AA======G===GGG
= Usage =
= Usage =
