Examples of picard.annotation.Gene.Transcript

                throw new AnnotationException("Chromosome disagreement(" + chromosome + " != " + row.getField(RefFlatColumns.CHROMOSOME.name()) +
                                                      ") in refFlat file for gene " + geneName);
            }


            // This adds it to the Gene also
            final Transcript tx = makeTranscriptFromRefFlatLine(gene, row);
        }


        return gene;
    }

        final int transcriptionStart = row.getIntegerField(RefFlatColumns.TX_START.name()) + 1;
        final int transcriptionEnd = row.getIntegerField(RefFlatColumns.TX_END.name());
        final int codingStart = row.getIntegerField(RefFlatColumns.CDS_START.name()) + 1;
        final int codingEnd = row.getIntegerField(RefFlatColumns.CDS_END.name());


        final Transcript tx = gene.addTranscript(transcriptName, transcriptionStart, transcriptionEnd, codingStart, codingEnd, exonCount);


        for (int i = 0; i < exonCount; ++i) {
            final Exon e = tx.addExon(Integer.parseInt(exonStarts[i]) + 1, Integer.parseInt(exonEnds[i]));


            if (e.start >= e.end) {
                throw new AnnotationException("Exon has 0 or negative extent for " + transcriptDescription);
            }
            if (i > 0 && tx.exons[i-1].end >= tx.exons[i].start) {

Related Classes of picard.annotation.Gene.Transcript

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