Examples with CreateSequenceDictionary picard.sam.CreateSequenceDictionary used on opensource projects

Example 1 with CreateSequenceDictionary

use of picard.sam.CreateSequenceDictionary in project gridss by PapenfussLab.

the class MultipleSamFileCommandLineProgram method ensureSequenceDictionary.

public static void ensureSequenceDictionary(File fa) throws IOException {
    File output = new File(fa.getAbsolutePath() + ".dict");
    try (ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(fa)) {
        SAMSequenceDictionary dictionary = reference.getSequenceDictionary();
        if (dictionary == null) {
            log.info("Attempting to generate missing sequence dictionary for ", fa);
            try {
                final SAMSequenceDictionary sequences = new CreateSequenceDictionary().makeSequenceDictionary(fa);
                final SAMFileHeader samHeader = new SAMFileHeader();
                samHeader.setSequenceDictionary(sequences);
                try (SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(samHeader, false, output)) {
                }
            } catch (Exception e) {
                log.error("Missing sequence dictionary for ", fa, " and creation of sequencing dictionary failed.", "Please run the Picard tools CreateSequenceDictionary utility to create", output);
                throw e;
            }
            log.info("Created sequence dictionary ", output);
        } else {
            log.debug("Found sequence dictionary for ", fa);
        }
    }
}