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==== Bam Format ====
==== SAM/Bam Format ====
use .bam extension to output in BAM format instead of diff format.
use .sam/.bam extension to output in SAM/BAM format instead of diff format.
In BAM format there will be 3 output files:
In SAM/BAM format there will be 3 output files:
# the specified name with record diffs
# the specified name with record diffs
# specified name with _only_<in1>.bam with records only in the in1 file
# specified name with _only_<in1>.b(s)am with records only in the in1 file
# specified name with _only_<in2>.bam with records only in the in2 file
# specified name with _only_<in2>.b(s)am with records only in the in2 file
When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags:
