Reverts the original base qualities and adds the mate cigar tag to read-group BAMs.
java -jar picard.jar RevertOriginalBaseQualitiesAndAddMateCigar
INPUT (File) The input SAM/BAM file to revert the state of. Required.
OUTPUT (File) The output SAM/BAM file to create. Required.
SORT_ORDER (SortOrder) The sort order to create the reverted output file with.By default, the sort order will be the same as the input. Default value: null. Possible values: {unsorted, queryname, coordinate, duplicate}
RESTORE_ORIGINAL_QUALITIES (Boolean) True to restore original qualities from the OQ field to the QUAL field if available. Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
MAX_RECORDS_TO_EXAMINE (Integer) The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the file. Default value: 10000. This option can be set to 'null' to clear the default value.