--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.datamodel.CigarParser;
+import jalview.datamodel.Range;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.PrimitiveIterator.OfInt;
+import java.util.SortedMap;
+
+import htsjdk.samtools.SAMRecord;
+import htsjdk.samtools.SAMRecordIterator;
+import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.SamInputResource;
+import htsjdk.samtools.SamReader;
+import htsjdk.samtools.SamReaderFactory;
+import htsjdk.samtools.ValidationStringency;
+
+public class BamFile extends AlignFile
+{
+ // SAM/BAM file reader
+ private SamReader fileReader;
+
+ // start position to read from
+ private int start = -1;
+
+ // end position to read to
+ private int end = -1;
+
+ // chromosome/contig to read
+ private String chromosome = "";
+
+ // first position in alignment
+ private int alignmentStart = -1;
+
+ /**
+ * Creates a new BamFile object.
+ */
+ public BamFile()
+ {
+ }
+
+ /**
+ * Creates a new BamFile object.
+ *
+ * @param inFile
+ * Name of file to read
+ * @param sourceType
+ * Whether data source is file, url or other type of data source
+ *
+ * @throws IOException
+ */
+ public BamFile(String inFile, DataSourceType sourceType)
+ throws IOException
+ {
+ super(true, inFile, sourceType);
+ final SamReaderFactory factory = SamReaderFactory.makeDefault()
+ .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
+ SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
+ .validationStringency(ValidationStringency.SILENT);
+ fileReader = factory.open(new File(inFile));
+ }
+
+ /**
+ * Creates a new BamFile object
+ *
+ * @param source
+ * wrapper for datasource
+ * @throws IOException
+ */
+ public BamFile(FileParse source) throws IOException
+ {
+ super(true, source);
+ parseSuffix();
+ final SamReaderFactory factory = SamReaderFactory.makeDefault()
+ .enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS,
+ SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS)
+ .validationStringency(ValidationStringency.SILENT);
+
+ // File-based bam
+ if (source.getDataSourceType() == DataSourceType.FILE)
+ {
+ fileReader = factory.open(source.inFile);
+ }
+ else
+ {
+ // locate index ?
+ String index = source.getDataName() + ".bai";
+ fileReader = factory.open(SamInputResource.of(source.getDataName())
+ .index(new URL(index)));
+ }
+ }
+
+ @Override
+ public String print(SequenceI[] seqs, boolean jvsuffix)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ private StringBuilder insertRefSeq(
+ SortedMap<Integer, Integer> insertions, Range xtent)
+ {
+ StringBuilder refseq = new StringBuilder();
+ int inserted = 0;
+ for (int p = xtent.start; p < xtent.end; p++)
+ {
+ refseq.append('N');
+ }
+ for (Map.Entry<Integer, Integer> insert : insertions.entrySet())
+ {
+ int inspos = insert.getKey() - xtent.start + inserted;
+ if (inspos < 0)
+ {
+ System.out.println("Ignoring -ve insert position " + insert.getKey()
+ + " of " + insert.getValue() +
+ " (alpos: " + inspos + ")");
+ inspos = 0;
+ // continue;
+ }
+ for (int i = 0, j = insert.getValue(); i < j; i++)
+ {
+ inserted++;
+ refseq.insert(inspos, '-');
+ }
+ }
+ return refseq;
+ }
+
+ private void padRef(SequenceI ref, CigarParser cig)
+ { // pad to column
+ int padding = cig.firstAlColumn - ref.findIndex(cig.firstRposCol);
+ System.out.println("Padding " + padding + " to move refseq position "
+ + cig.firstRposCol + " to " + cig.firstAlColumn + "col.");
+
+ ref.insertCharAt(0, padding, '-');
+ }
+
+ @Override
+ public void parse()
+ {
+ // only actually parse if params are set
+ if (chromosome != null && chromosome != "")
+ {
+ SAMRecordIterator it = fileReader.query(chromosome, start, end,
+ false);
+ CigarParser parser = new CigarParser('-');
+ Range[] xtent = new Range[] { new Range(start, end) };
+ SortedMap<Integer, Integer> insertions[] = parser.getInsertions(it,
+ xtent);
+ it.close();
+
+ SequenceI refSeq = new Sequence("chr:" + chromosome,
+ insertRefSeq(insertions[0], xtent[0])
+ .toString());
+
+ refSeq.setStart(xtent[0].start);
+ refSeq.setEnd(xtent[0].end);
+ SequenceI revRefSeq = new Sequence("rev:chr:" + chromosome,
+ insertRefSeq(insertions[1], xtent[0])
+ .toString());
+ revRefSeq.setStart(xtent[0].start);
+ revRefSeq.setEnd(xtent[0].end);
+
+ // Hack to move the seqs along
+ padRef(refSeq, parser);
+ padRef(revRefSeq, parser);
+
+ it = fileReader.query(chromosome, start, end, false);
+
+ ArrayList<SequenceI> fwd = new ArrayList(), rev = new ArrayList();
+ while (it.hasNext())
+ {
+ SAMRecord rec = it.next();
+
+ // set the alignment start to be start of first read (we assume reads
+ // are sorted)
+ if (alignmentStart == -1)
+ {
+ alignmentStart = rec.getAlignmentStart();
+ }
+
+ // make dataset sequence: start at 1, end at read length
+ SequenceI seq = new Sequence(
+ "" + (rec.getReadNegativeStrandFlag() ? "rev:" : "")
+ + rec.getReadName(),
+ rec.getReadString().toLowerCase());
+ seq.setStart(1);
+ seq.setEnd(rec.getReadLength());
+ OfInt q = rec.getBaseQualityString().chars()
+ .iterator();
+ int p = seq.getStart();
+ while (q.hasNext())
+ {
+ seq.addSequenceFeature(new SequenceFeature("QUALITY", "", p, p,
+ (float) q.next() - ' ', "bamfile"));
+ p++;
+ }
+ String newRead = parser.parseCigarToSequence(rec,
+ insertions[rec.getReadNegativeStrandFlag() ? 1 : 0],
+ alignmentStart, seq);
+
+ // make alignment sequences
+ SequenceI alsq = seq.deriveSequence();
+ alsq.setSequence(newRead);
+
+ // set start relative to soft clip; assume end is set by Sequence code
+ alsq.setStart(rec.getStart() - rec.getUnclippedStart() + 1);
+ if (rec.getReadNegativeStrandFlag())
+ {
+ rev.add(alsq);
+ }
+ else
+ {
+ fwd.add(alsq);
+ }
+ }
+ // Add forward
+ if (fwd.size() > 0)
+ {
+ seqs.add(refSeq); // FIXME needs to be optional, and properly padded
+ seqs.addAll(fwd);
+ fwd.clear();
+ }
+ // and reverse strand reads.
+ if (rev.size() > 0)
+ {
+ seqs.add(revRefSeq); // FIXME needs to be optional and properly padded
+ seqs.addAll(rev);
+ rev.clear();
+ }
+ }
+ }
+
+ /**
+ * Get the list of chromosomes or contigs from the file (listed in SQ entries
+ * in BAM file header)
+ *
+ * @return array of chromosome/contig strings
+ */
+ @Override
+ public Object[] preprocess()
+ {
+ List<SAMSequenceRecord> refSeqs = fileReader.getFileHeader()
+ .getSequenceDictionary().getSequences();
+ List<String> chrs = new ArrayList<>();
+
+ for (SAMSequenceRecord ref : refSeqs)
+ {
+ chrs.add(ref.getSequenceName());
+ }
+ return chrs.toArray();
+ }
+
+ public void setOptions(String chr, int s, int e)
+ {
+ chromosome = chr;
+ start = s;
+ end = e;
+ suffix = chromosome + ":" + start + "-" + end;
+ }
+
+ public boolean parseSuffix()
+ {
+ if (suffix == null)
+ {
+ return false;
+ }
+ int csep = suffix.indexOf(":");
+ int rsep = suffix.indexOf("-", csep);
+ if (csep < 0 || rsep < 0 || suffix.length() - rsep <= 1)
+ {
+ return false;
+ }
+ String chr, p1, p2;
+ chr = suffix.substring(0, csep);
+ p1 = suffix.substring(csep + 1, rsep);
+ p2 = suffix.substring(rsep + 1);
+ int cstart, cend;
+ try
+ {
+ cstart = Integer.parseInt(p1);
+ cend = Integer.parseInt(p2);
+ } catch (Exception e)
+ {
+ warningMessage = (warningMessage == null ? "" : warningMessage + "\n")
+ + "Couldn't parse range from " + suffix;
+ return false;
+ }
+ chromosome = chr;
+ start = cstart;
+ end = cend;
+ return true;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff