diff --git a/ChangeLog b/ChangeLog
index 1e93637250467ab05b0f473206b20f593bcbac0e..ac4dd048395daa01284b23dad4492a9d26cf6eb6 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -32,7 +32,8 @@ Version XX
Added RNASeq strand specific option to the BAM popup menu ('Colour By' ->
'RNASeq Strand Specific Tag (XS)'). Reads colours are based on the XS
- tag (used by TopHat). The RNA strand is then used in the coverage plots.
+ tag (used by TopHat). The RNA strand is then used in the coverage plots
+ and in calculation of read counts and RPKM values.
Added the following flags:
-Dshow_snps Show SNP marks in BamView
diff --git a/etc/versions b/etc/versions
index 421ae9799d4195db9eaba97fbcc4226e4b96109b..9554acd842830fd4a4ffb8cf976daaf615dc3fa4 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 15.1.10
-ACT Release 12.1.10
+Artemis Release 15.1.11
+ACT Release 12.1.11
DNAPlotter Release 1.11
BamView 1.2.10
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 444080cdba525688245711c67a5080b79db333e8..8e00d327128cbc1ff1bdb3bc4b3b0cbfd74ac425 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -1343,7 +1343,16 @@ public class ChadoTransactionManager
}
// get the cvterm_id for this featureprop/qualifier
- Integer lcvterm_id = DatabaseDocument.getCvtermID(name);
+ CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(name, "feature_property");
+ Integer lcvterm_id;
+ if(cvterm != null)
+ lcvterm_id = cvterm.getCvTermId();
+ else
+ lcvterm_id = DatabaseDocument.getCvtermID(name);
+
+ if(lcvterm_id == null)
+ lcvterm_id = DatabaseDocument.getCvtermID(name);
+
if(lcvterm_id == null) // chado doesn't recognise this
{
JOptionPane.showMessageDialog(null,
@@ -1406,7 +1415,11 @@ public class ChadoTransactionManager
Integer lcvterm_id = null;
if(!name.equals("timelastmodified"))
{
- lcvterm_id = DatabaseDocument.getCvtermID(name);
+ CvTerm cvterm = DatabaseDocument.getCvTermByCvAndCvTerm(name, "feature_property");
+ if(cvterm != null)
+ lcvterm_id = cvterm.getCvTermId();
+ else
+ lcvterm_id = DatabaseDocument.getCvtermID(name);
if(lcvterm_id == null) // chado doesn't recognise this
{
diff --git a/uk/ac/sanger/artemis/components/alignment/BamUtils.java b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
index 8f7c017c33b55f18c220186ea4c9acfb3e6ead66..c064061f317bf05844cb67b532257fc5756b42b8 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -65,6 +65,7 @@ class BamUtils
* @param samRecordFlagPredicate
* @param samRecordMapQPredicate
* @param contained
+ * @param useStrandTag - strand specific tag
* @return
*/
protected static float[] getCount(
@@ -79,7 +80,8 @@ class BamUtils
final HashMap<String, Integer> seqLengths,
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordMapQPredicate samRecordMapQPredicate,
- final boolean contained)
+ final boolean contained,
+ final boolean useStrandTag)
{
int cnt[] = new int[2];
cnt[0] = 0;
@@ -107,7 +109,7 @@ class BamUtils
thisEnd = thisLength;
cnt = count(bam, samFileReaderHash, name, thisStart, thisEnd,
- samRecordFlagPredicate, samRecordMapQPredicate, contained, true);
+ samRecordFlagPredicate, samRecordMapQPredicate, contained, true, useStrandTag);
}
lastLen = len;
@@ -116,7 +118,7 @@ class BamUtils
else
{
cnt = count(bam, samFileReaderHash, refName, start, end,
- samRecordFlagPredicate, samRecordMapQPredicate, contained, true);
+ samRecordFlagPredicate, samRecordMapQPredicate, contained, true, useStrandTag);
}
float cntf[] = new float[2];
@@ -133,7 +135,8 @@ class BamUtils
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordPredicate samRecordMapQPredicate,
final boolean contained,
- final boolean byStrand)
+ final boolean byStrand,
+ final boolean useStrandTag)
{
int cnt[] = new int[2];
cnt[0] = 0;
@@ -151,7 +154,7 @@ class BamUtils
if(samRecordMapQPredicate == null ||
samRecordMapQPredicate.testPredicate(samRecord))
{
- if(byStrand && samRecord.getReadNegativeStrandFlag())
+ if(byStrand && BamView.isNegativeStrand(samRecord, useStrandTag))
cnt[1]++;
else
cnt[0]++;
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 6b6275c238e22cd0cf08f19a171d4121944b6cd5..ed133c2cf02ec9ad4c1667e7fc1b7045c98e44cc 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -1623,7 +1623,7 @@ public class BamView extends JPanel
for(BamViewRecord bamViewRecord: readsInView)
{
SAMRecord samRecord = bamViewRecord.sam;
- if( isNegativeStrand(samRecord) == isStrandNegative )
+ if( isNegativeStrand(samRecord, colourByStrandTag.isSelected()) == isStrandNegative )
{
final int offset = getSequenceOffset(samRecord.getReferenceName());
final int recordStart = samRecord.getAlignmentStart()+offset;
@@ -1847,11 +1847,13 @@ public class BamView extends JPanel
* Check if a record is on the negative strand. If the RNA strand specific
* checkbox is set then use the RNA strand.
* @param samRecord
+ * @param useStrandTag - strand specific tag
* @return
*/
- private boolean isNegativeStrand(final SAMRecord samRecord)
+ protected static boolean isNegativeStrand(final SAMRecord samRecord,
+ final boolean useStrandTag)
{
- if(colourByStrandTag.isSelected())
+ if(useStrandTag)
{
if(samRecord.getAttribute("XS") == null)
return samRecord.getReadNegativeStrandFlag();
@@ -2583,7 +2585,7 @@ public class BamView extends JPanel
new MappedReads(features, (String)combo.getSelectedItem(), samFileReaderHash, bamList,
seqNames, offsetLengths, concatSequences, seqLengths,
samRecordFlagPredicate, samRecordMapQPredicate,
- !overlap.isSelected(), spliced.isSelected());
+ !overlap.isSelected(), spliced.isSelected(), colourByStrandTag.isSelected());
}
});
@@ -2623,7 +2625,8 @@ public class BamView extends JPanel
new MappedReads(features, (String)combo.getSelectedItem(),
samFileReaderHash, bamList, seqNames, offsetLengths, concatSequences,
seqLengths, seqlen, samRecordFlagPredicate, samRecordMapQPredicate,
- !overlap.isSelected(), spliced.isSelected(), allRefSeqs.isSelected());
+ !overlap.isSelected(), spliced.isSelected(), allRefSeqs.isSelected(),
+ colourByStrandTag.isSelected());
}
});
diff --git a/uk/ac/sanger/artemis/components/alignment/MappedReads.java b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
index e51f5f0cc98c49e6baae68d19fda195542d6d297..7b13366f24db748b3fe0ebed063be798eb3898d0 100644
--- a/uk/ac/sanger/artemis/components/alignment/MappedReads.java
+++ b/uk/ac/sanger/artemis/components/alignment/MappedReads.java
@@ -58,6 +58,7 @@ public class MappedReads
private SAMRecordMapQPredicate samRecordMapQPredicate;
private boolean contained;
private boolean useIntrons;
+ private boolean useStrandTag = false;
private JDialog dialog = new JDialog((JFrame)null, "Calculating", true);;
private int mappedReads[];
@@ -87,7 +88,8 @@ public class MappedReads
SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained,
final boolean useIntrons,
- final boolean allRefSeqs)
+ final boolean allRefSeqs,
+ final boolean useStrandTag)
{
this.features = features;
this.refName = refName;
@@ -102,6 +104,7 @@ public class MappedReads
this.samRecordMapQPredicate = samRecordMapQPredicate;
this.contained = contained;
this.useIntrons = useIntrons;
+ this.useStrandTag = useStrandTag;
progressBar = new JProgressBar(0, sequenceLength);
progressBar.setValue(0);
@@ -150,7 +153,8 @@ public class MappedReads
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained,
- final boolean useIntrons)
+ final boolean useIntrons,
+ final boolean useStrandTag)
{
this.features = features;
this.refName = refName;
@@ -164,6 +168,7 @@ public class MappedReads
this.samRecordMapQPredicate = samRecordMapQPredicate;
this.contained = contained;
this.useIntrons = useIntrons;
+ this.useStrandTag = useStrandTag;
progressBar = new JProgressBar(0, features.size());
progressBar.setValue(0);
@@ -297,7 +302,7 @@ public class MappedReads
float tmpcnt[] = new float[2];
tmpcnt = BamUtils.getCount(start, end, bam, refName, samFileReaderHash,
seqNames, offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate, contained);
+ samRecordFlagPredicate, samRecordMapQPredicate, contained, useStrandTag);
cnt[0] += tmpcnt[0];
cnt[1] += tmpcnt[1];
}
@@ -305,7 +310,7 @@ public class MappedReads
else
cnt = BamUtils.getCount(start, end, bam, refName, samFileReaderHash, seqNames,
offsetLengths, concatSequences, seqLengths,
- samRecordFlagPredicate, samRecordMapQPredicate, contained);
+ samRecordFlagPredicate, samRecordMapQPredicate, contained, useStrandTag);
if (mappedReads != null)
{
@@ -543,7 +548,7 @@ public class MappedReads
mappedReads[j] += BamUtils.count(bam, samFileReaderHash, name,
thisStart, thisEnd, samRecordFlagPredicate,
- samRecordMapQPredicate, contained, false)[0];
+ samRecordMapQPredicate, contained, false, useStrandTag)[0];
}
lastLen = len;
@@ -553,7 +558,7 @@ public class MappedReads
{
mappedReads[j] += BamUtils.count(bam, samFileReaderHash, refName, sbegc,
sendc, samRecordFlagPredicate, samRecordMapQPredicate,
- contained, false)[0];
+ contained, false, useStrandTag)[0];
}
}
}