This mode is used to extract reads from a SAM/BAM file. It is implemented by edu.cornell.med.icb.goby.modes.SamExtractReadsMode.java.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
(-o|--output)outputnoWhere the output will be written.
n/ainputyesThe SAM input file.
--quality-encodingquality-encodingnoThe encoding for quality scores. The default quality encoding is to not convert the characters (BAM encoding). Valid encodings include BAM, Illumina, Sanger and Solexa. Default value: BAM