This mode is used to compare two sam/bam files. It was introduced in Goby 2.0. It is useful to check that converting sam->goby->sam works well.

It is implemented by edu.cornell.med.icb.goby.modes.SamComparisonMode.java.

FlagArgumentsRequiredDescription
(-s|--source-bam)source-bamyesThe original SAM/BAM file that was converted from.
(-d|--destination-bam)destination-bamyesThe SAM/BAM file that was converted to.
(-g|--destination-goby)destination-gobynoThe Goby Compact Alignment file that was converted to (inclusion of this flag will increase the amount of provided mismatch output).
--mapped-qualities-preservedmapped-qualities-preservednoWhen this switch is provided, the destination Goby Compact Alignment was created with –preserve-all-mapped-qualities so all quality scores will be verified. By default, only the bases that have sequence variations will be verified. Default value: false
--check-matecheck-matenoWhen this switch is provided, source SAM/BAM file is known to be complete (not a subset of a larger SAM/BAM file) and mate/pair details will be validated. By default, mate/pair details are NOT checked because with incomplete SAM/BAM files, the converted Goby Compact Alignment file may not contain details about pairs that were not found in the incomplete source SAM/BAM file. Default value: false
--soft-clips-preservedsoft-clips-preservednoWhen this switch is provided, the destination Goby Compact Alignment was created with –preserve-soft-clips so the clipped bases will be verified. By default, only the aligned bases will be verified. Default value: false
--canonical-mdzcanonical-mdznoWhen true, the source and destination MD:Z values will be passed through an algorithm to make them canonical (place 0’s in places where 0’s should exist but might not). By default this is enabled. Default value: true
-xdynamic-optionsnoSet a dynamic option, in the format classname:key=value. Classname is the the name of the class that exposes the option (short class name without package), key identifies the option to change and value is the new value for the option.