This mode is used to convert Goby alignments to SAM or BAM format. It is implemented by edu.cornell.med.icb.goby.modes.CompactToSamMode.java.

See this tutorial for details about how to use sam-to-compact.

Mode Parameters

The following options are available in this mode

FlagArgumentsRequiredDescription
n/ainput-basenameyesThe compact alignment file to read as input.
(-o|--output)outputyesThe SAM/BAM output file to output to. Please note that if the file ends in .bam, a BAM file will be written, whereas if the file ends in .sam, a BAM file will be written instead.
(-g|--genome)input-genomeyesThe input genome in either ‘compact random-access-genome’ format or ‘fa + fa.fai’ format. The random-access-genome file can be made from a fasta reference using the build-sequence-cache mode. If using the random-access-genome input, specify any one of the files in the random-access-genome. If using the ‘.fa + .fa.fai’ input, specify the ‘.fa’ file but make sure the ‘.fa.fai’ file is located in the same directory. Using the random-access-genome format can be considerably faster, but uses more memory than using the picard indexed fasta file.
(-r|--include-reference-names)include-reference-namesnoWhen provided, only process reference identifiers listed in this comma separated list. To process only chromosome 19 and 1, if sequences are identified by 1 and 19, use: –include-reference-names 1,19
--quality-encodingquality-encodingnoThe encoding for quality scores. The default quality encoding is set to Sanger/Phred as per BAM/SAM specification v1.4-r985. Valid encodings include Illumina, Phred=Sanger and Solexa. Default value: Phred
-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.