SAMToGBSdbPlugin reads a SAM file to determine the potential positions of Tags against the reference genome. The plugin updates the current database with information on tag cut positions. It will throw an error if there are tags found in the SAM file that can not be matched to tags in the database.

The parameters to this plugin are:

• -aLen< Minimum length of aligned base pair to store the SAM entry> (Default is 0)
• -aProp <Minimum proportion of sequence that must align to store the SAM entry> (Default is 0)
• -i <SAM Input file> (REQUIRED)
• -db <GBS DB file> (REQUIRED)
• -minMAPQ < Minimum value of MAPQ field to store the SAM entry > (Default is 0)
• -deleteOldData <true | false> If value is "true", database tables populated from this step and subsequent steps of the GBSv2 pipeline are cleared. This removes all data related to tag cur positions, SNPs and SNPQuality and allows for re-running the pipeline with a new data from this step. (Default: true)

Both the minAlignmentLength and minAlignProportion code check the MD value (regex String for mismatching positions) for number of positions in the sequence that match the reference. The CIGAR value is used if MD is not available. This number is used to determine if the tag meets the minAlignmentLength/Proportion specified by the user. If they do not, the tag will be stored in the database without this corresponding position.

A high value for Minimum length aligned or minimum proportion aligned will result in fewer cut positions stored against tags in the database. A default of 0 should be used for both if the desire is to have all tags/positions included.

The minMAPQ parameter can be used to limit filter low quality SNPs before storing in the database.

If tags exist in the .sam file which are not found in the database, the data is considered inconsistent and no alignments are added to the database tables.

To run this command from the command line:

#!java

./run_pipeline.pl -fork1 -SAMToGBSdbPlugin 
-i /Users/lcj34/git/tassel-5-test/tempDir/GBS/Chr9_10-20000000/tagsForAlign910auto.sam 
-db /Users/lcj34/git/tassel-5-test/tempDir/GBS/Chr9_10-20000000/GBSv2.db 
-aProp 0.0 -aLen 0 -endPlugin -runfork1

To call the SAMToGBSdbPlugin from program code:

#!java

            new SAMToGBSdbPlugin()
                .gBSDBFile(GBSConstants.GBS_GBS2DB_FILE)
                .sAMInputFile(inTagSAM)
                .minAlignLength(0)
                .minAlignProportion(0.0)
                .performFunction(null);