From 2c326dc94cff8ef0e83333ba1d17897fcd787f86 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 27 Mar 2012 17:01:52 +0100
Subject: [PATCH] reference sequence file for CRAM format
---
.../alignment/CRAMReferenceSequenceFile.java | 111 ++++++++++++++++++
1 file changed, 111 insertions(+)
create mode 100644 uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
diff --git a/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java b/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
new file mode 100644
index 000000000..ae2fb2d72
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
@@ -0,0 +1,111 @@
+/* BamView
+ *
+ * created: 2012
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2012 Genome Research Limited
+ *
+ * This program 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 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
+ *
+ */
+package uk.ac.sanger.artemis.components.alignment;
+
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.samtools.SAMSequenceDictionary;
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.io.Range;
+import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+
+
+ class CRAMReferenceSequenceFile implements ReferenceSequenceFile
+ {
+ private Entry sequence;
+ private BamView bamView;
+
+ CRAMReferenceSequenceFile(final Entry sequence, final BamView bamView)
+ {
+ this.sequence = sequence;
+ this.bamView = bamView;
+ }
+
+ /**
+ * Retrieves the complete sequence described by this contig.
+ * @param contig contig whose data should be returned.
+ * @return The full sequence associated with this contig.
+ * @throws UnsupportedOperationException if !sIndexed.
+ */
+ public ReferenceSequence getSequence(String contig)
+ {
+ return getSubsequenceAt(contig, 1L, sequence.getBases().getLength());
+
+ //return new ReferenceSequence(sequence.getName(), 0,
+ // sequence.getBases().getForwardStrand().getStrandBases().getBytes());
+ }
+
+ public SAMSequenceDictionary getSequenceDictionary()
+ {
+ return null;
+ }
+
+ /**
+ * Gets the subsequence of the contig in the range [start,stop]
+ * @param contig Contig whose subsequence to retrieve.
+ * @param start inclusive, 1-based start of region.
+ * @param stop inclusive, 1-based stop of region.
+ * @return The partial reference sequence associated with this range.
+ * @throws UnsupportedOperationException if !sIndexed.
+ */
+ public ReferenceSequence getSubsequenceAt(String contig, long start, long stop )
+ {
+ try
+ {
+ if(bamView.isConcatSequences())
+ {
+ int offset = bamView.getSequenceOffset(contig);
+ start += offset;
+ stop += offset;
+ }
+
+ return new ReferenceSequence(sequence.getName(), 0,
+ sequence.getBases().getSubSequence(new Range((int)start, (int)stop), Bases.FORWARD).getBytes());
+ }
+ catch (OutOfRangeException e)
+ {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ /**
+ * @return true if getSequence and getSubsequenceAt methods are allowed.
+ */
+ public boolean isIndexed()
+ {
+ return true;
+ }
+
+ public ReferenceSequence nextSequence()
+ {
+ return null;
+ }
+
+ public void reset()
+ {
+ }
+
+ }
\ No newline at end of file
--
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