Examples of AlignmentIndexer

Examples of org.broad.igv.sam.reader.AlignmentIndexer

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        File outputFile = new File(outputFileName);

        //Sam/FASTA files are special
        try {
            if (typeString.endsWith("sam")) {
                AlignmentIndexer indexer = AlignmentIndexer.getInstance(inputFile, null, null);
                indexer.createSamIndex(outputFile);
                return outputFileName;
            } else if (isFasta) {
                FastaUtils.createIndexFile(inputFile.getAbsolutePath(), outputFileName);
                return outputFileName;
            }
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Examples of org.broad.igv.sam.reader.AlignmentIndexer

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    }

    public class SamIndexWorker extends IndexWorker<FeatureIndex> {
        @Override
        protected FeatureIndex doInBackground() throws Exception {
            AlignmentIndexer indexer = AlignmentIndexer.getInstance(file, progressBar, this);
            return indexer.createSamIndex(idxFile, 16000);
        }
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