Changes

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 '='.

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 '='.

==== Example ====

==== Examples ====

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

Sequence:      AATAA  CTAGA  T AGGG

Sequence:      AATAA  CTAGA  T AGGG

Reference:      TAACCCTA ACCCT A

Reference:      TAACCCTA ACCCT A

Sequence with Orig:  AATAACTAGATAGGG

Sequence with Orig:  AATAACTAGATAGGG

Sequence with Bases:  AATAACTAGATAGGG

Sequence with Bases:  AATAACTAGATAGGG

Sequence with Equals: AA======G===GGG

Sequence with Equals: AA======G===GGG

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

Sequence:      AATGA  CTGGA  T AGGG

Sequence:      AATGA  CTGGA  T AGGG

Reference:      TAACCCTA ACCCT A

Reference:      TAACCCTA ACCCT A

Sequence with Orig:  AATGACTGGATAGGG

Sequence with Orig:  AATGACTGGATAGGG

Sequence with Bases:  AATGACTGGATAGGG

Sequence with Bases:  AATGACTGGATAGGG

Sequence with Equals: AA=G===GG===GGG

Sequence with Equals: AA=G===GG===GGG

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

Sequence:      AAT=A  CT=GA  T AGGG

Sequence:      AAT=A  CT=GA  T AGGG

Reference:      TAACCCTA ACCCT A

Reference:      TAACCCTA ACCCT A

Sequence with Orig:  AAT=ACT=GATAGGG

Sequence with Orig:  AAT=ACT=GATAGGG

Sequence with Bases:  AATGACTGGATAGGG

Sequence with Bases:  AATGACTGGATAGGG

Sequence with Equals: AA======G===GGG

Sequence with Equals: AA======G===GGG

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

ExtendedCigar: SSMMMDDMMMIMNNNMPMSSS

Sequence:      AA===  ===G=  = =GGG

Sequence:      AA===  ===G=  = =GGG

Reference:      TAACCCTA ACCCT A

Reference:      TAACCCTA ACCCT A

Sequence with Orig:  AA======G===GGG

Sequence with Orig:  AA======G===GGG

Sequence with Bases:  AATAACTAGATAGGG

Sequence with Bases:  AATAACTAGATAGGG

Sequence with Equals: AA======G===GGG

Sequence with Equals: AA======G===GGG

=== Parameters ===

=== Parameters ===