2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.datamodel.CigarParser;
24 import jalview.datamodel.Sequence;
25 import jalview.datamodel.SequenceI;
28 import java.io.IOException;
29 import java.util.SortedMap;
31 import htsjdk.samtools.SAMRecord;
32 import htsjdk.samtools.SAMRecordIterator;
33 import htsjdk.samtools.SamReader;
34 import htsjdk.samtools.SamReaderFactory;
35 import htsjdk.samtools.ValidationStringency;
37 public class BamFile extends AlignFile
43 * Creates a new BamFile object.
50 * Creates a new BamFile object.
60 public BamFile(String inFile, DataSourceType sourceType)
63 super(inFile, sourceType);
64 final SamReaderFactory factory = SamReaderFactory.makeDefault()
65 .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
66 SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
67 .validationStringency(ValidationStringency.SILENT);
68 fileReader = factory.open(new File(inFile));
71 public BamFile(FileParse source) throws IOException
73 final SamReaderFactory factory = SamReaderFactory.makeDefault()
74 .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
75 SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
76 .validationStringency(ValidationStringency.SILENT);
79 fileReader = factory.open(source.inFile);
84 public String print(SequenceI[] seqs, boolean jvsuffix)
86 // TODO Auto-generated method stub
91 public void parse() throws IOException
93 SAMRecordIterator it = fileReader.iterator();
94 CigarParser parser = new CigarParser('-');
95 SortedMap<Integer, Integer> insertions = parser.getInsertions(it);
98 it = fileReader.iterator();
101 SAMRecord rec = it.next();
103 // make dataset sequence: start at 1, end at read length
104 SequenceI seq = new Sequence(rec.getReadName(),
105 rec.getReadString().toLowerCase());
107 seq.setEnd(rec.getReadLength());
109 String newRead = parser.parseCigarToSequence(rec, insertions);
111 // make alignment sequences
112 SequenceI alsq = seq.deriveSequence();
113 alsq.setSequence(newRead);
115 // set start relative to soft clip; assume end is set by Sequence code
116 alsq.setStart(rec.getStart() - rec.getUnclippedStart() + 1);