Examples of SAMFileWriterFactory

Examples of htsjdk.samtools.SAMFileWriterFactory

61
62
63
64
65
66
67
68
69
70
71
    public int execute() {
        long readsWritten = 0;
        long readsAltered = 0;

        SAMFileReader reader = new SAMFileReader(input);
        SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(),true,output,compressionLevel);

        for(SAMRecord read: reader) {
            Object value = read.getAttribute(sourceTagName);
            if(value != null) {
                read.setAttribute(sourceTagName,null);
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

58
59
60
61
62
63
64
65
66
67
68
69
70
            tempFile = File.createTempFile("testfile_"+getMaxReads(),".bam");
        }
        catch(IOException ex) {
            throw new ReviewedGATKException("Unable to create temporary BAM",ex);
        }
        SAMFileWriterFactory factory = new SAMFileWriterFactory();
        factory.setCreateIndex(true);
        SAMFileWriter writer = factory.makeBAMWriter(fullInputFile.getFileHeader(),true,tempFile);

        long numReads = 0;
        for(SAMRecord read: fullInputFile) {
            if(numReads++ >= getMaxReads())
                break;
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

76
77
78
79
80
81
82
83
84
85
86
        if (VALIDATION_STRINGENCY == ValidationStringency.STRICT) {
            SAMFileReader.setDefaultValidationStringency(ValidationStringency.LENIENT);
        }
        try {
            final SAMFileReader reader = new SAMFileReader(INPUT);
            final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);
            final CloseableIterator<SAMRecord> it = reader.iterator();
            final ProgressLogger progress = new ProgressLogger(Log.getInstance(CleanSam.class));

            // If the read (or its mate) maps off the end of the alignment, clip it
            while(it.hasNext()) {
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

56
57
58
59
60
61
62
63
64
65
66
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

        final Random r = RANDOM_SEED == null ? new Random() : new Random(RANDOM_SEED);
        final SAMFileReader in = new SAMFileReader(INPUT);
        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(in.getFileHeader(), true, OUTPUT);
        final Map<String,Boolean> decisions = new HashMap<String,Boolean>();

        long total = 0;
        long kept  = 0;
       
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

195
196
197
198
199
200
201
202
203
204
205
        if (!REMOVE_ALIGNMENT_INFORMATION) {
            outHeader.setSequenceDictionary(inHeader.getSequenceDictionary());
            outHeader.setProgramRecords(inHeader.getProgramRecords());
        }

        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, presorted, OUTPUT);

        ////////////////////////////////////////////////////////////////////////////
        // Build a sorting collection to use if we are sanitizing
        ////////////////////////////////////////////////////////////////////////////
        final SortingCollection<SAMRecord> sorter;
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

104
105
106
107
108
109
110
111
112
113
114
        final SAMFileReader recordReader = new SAMFileReader(INPUT);
        if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
            throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
            ") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
        }
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);

        final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
        for (final SAMRecord rec : recordReader) {
            rec.setHeader(replacementHeader);
            writer.addAlignment(rec);
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

161
162
163
164
165
166
167
168
169
170
171
        IOUtil.assertFileIsReadable(FASTQ);
        IOUtil.assertFileIsWritable(OUTPUT);
       
        final FastqReader freader = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
        final SAMFileHeader header = createFileHeader();
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUTPUT);

        int readCount = 0;
        final ProgressLogger progress = new ProgressLogger(LOG);
        for ( ; freader.hasNext()  ; readCount++) {
            final FastqRecord frec = freader.next();
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

186
187
188
189
190
191
192
193
194
195
196
        IOUtil.assertFileIsWritable(OUTPUT);
       
        final FastqReader freader1 = new FastqReader(FASTQ,ALLOW_AND_IGNORE_EMPTY_LINES);
        final FastqReader freader2 = new FastqReader(FASTQ2,ALLOW_AND_IGNORE_EMPTY_LINES);
        final SAMFileHeader header = createFileHeader() ;
        final SAMFileWriter writer = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(header, false, OUTPUT);

        int readCount = 0;
        final ProgressLogger progress = new ProgressLogger(LOG);
        for ( ; freader1.hasNext() && freader2.hasNext() ; readCount++) {
            final FastqRecord frec1 = freader1.next();
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

85
86
87
88
89
90
91
92
93
94
95
        final SAMFileHeader outHeader = inHeader.clone();
        if (null == SORT_ORDER) this.SORT_ORDER = inHeader.getSortOrder(); // same as the input
        outHeader.setSortOrder(SORT_ORDER);
        SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(CREATE_INDEX);
        SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
        final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);

        // Iterate over the records, revert original base qualities, and push them into a SortingCollection by queryname
        final SortingCollection<SAMRecord> sorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(outHeader),
                new SAMRecordQueryNameComparator(), MAX_RECORDS_IN_RAM);
        final ProgressLogger revertingProgress = new ProgressLogger(log, 1000000, " reverted OQs");
View Full Code Here

Examples of htsjdk.samtools.SAMFileWriterFactory

148
149
150
151
152
153
154
155
156
157
158
        final SAMFileReader in = new SAMFileReader(INPUT);
        final SAMFileHeader.SortOrder order = in.getFileHeader().getSortOrder();
        SAMFileWriter out = null;
        if (OUTPUT != null) {
            IOUtil.assertFileIsWritable(OUTPUT);
            out = new SAMFileWriterFactory().makeSAMOrBAMWriter(in.getFileHeader(), true, OUTPUT);
        }

        final Histogram<Integer> histo = new Histogram<Integer>("clipped_bases", "read_count");

        // Combine any adapters and custom adapter pairs from the command line into an array for use in clipping
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.