Examples of org.broad.igv.feature.tribble.PSLCodec

org.broad.igv.feature.tribble.PSLCodec

@author jrobinso @date Aug 5, 2010

Columns:

1. matches - Number of bases that match that aren't repeats 2. misMatches - Number of bases that don't match 3. repMatches - Number of bases that match but are part of repeats 4. nCount - Number of 'N' bases 5. qNumInsert - Number of inserts in query 6. qBaseInsert - Number of bases inserted in query 7. tNumInsert - Number of inserts in target 8. tBaseInsert - Number of bases inserted in target 9. strand - '+' or '-' for query strand. For translated alignments, second '+'or '-' is for genomic strand 10. qName - Query sequence name 11. qSize - Query sequence size 12. qStart - Alignment start position in query 13. qEnd - Alignment end position in query 14. tName - Target sequence name 15. tSize - Target sequence size 16. tStart - Alignment start position in target 17. tEnd - Alignment end position in target 18. blockCount - Number of blocks in the alignment (a block contains no gaps) 19. blockSizes - Comma-separated list of sizes of each block 20. qStarts - Comma-separated list of starting positions of each block in query 21. tStarts - Comma-separated list of starting positions of each block in target

public class PSLAlignmentParser implements AlignmentParser {


    PSLCodec codec;


    public PSLAlignmentParser() {
        codec = new PSLCodec(); //genome);
    }


            public void run() {
                try {


                    Genome genome = IGV.hasInstance() ? GenomeManager.getInstance().getCurrentGenome() : null;
                    PSLCodec codec = new PSLCodec(genome, true);


                    // TODO -- something better than this!
                    String db = genome.getId();
                    String species = genome.getSpecies();
                    if (species == null) species = genome.getDisplayName();


                    List<String> tokensList = blat(species, db, userSeq);


                    // Convert tokens to features
                    List<PSLRecord> features = new ArrayList<PSLRecord>(tokensList.size());
                    for (String tokens : tokensList) {
                        PSLRecord f = codec.decode(tokens);
                        if (f != null) {
                            features.add(f);
                        }
                    }

Examples of org.broad.igv.feature.tribble.PSLCodec

Related Classes of org.broad.igv.feature.tribble.PSLCodec