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Commit d5fdac2c authored by tcarver's avatar tcarver
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report sense and antisense read counts and rpkm

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uk/ac/sanger/artemis/components/alignment/BamUtils.java
+ 22
− 11
View file @ d5fdac2c
......@@ -67,7 +67,7 @@ class BamUtils
* @param contained
* @return
*/
protected static int getCount(
protected static float[] getCount(
final int start,
final int end,
final String bam,
......@@ -81,7 +81,9 @@ class BamUtils
final SAMRecordMapQPredicate samRecordMapQPredicate,
final boolean contained)
{
int cnt = 0;
int cnt[] = new int[2];
cnt[0] = 0;
cnt[1] = 0;
if(concatSequences)
{
int len = 0;
......@@ -105,7 +107,7 @@ class BamUtils
thisEnd = thisLength;
cnt = count(bam, samFileReaderHash, name, thisStart, thisEnd,
samRecordFlagPredicate, samRecordMapQPredicate, contained);
samRecordFlagPredicate, samRecordMapQPredicate, contained, true);
}
lastLen = len;
......@@ -114,21 +116,29 @@ class BamUtils
else
{
cnt = count(bam, samFileReaderHash, refName, start, end,
samRecordFlagPredicate, samRecordMapQPredicate, contained);
samRecordFlagPredicate, samRecordMapQPredicate, contained, true);
}
return cnt;
float cntf[] = new float[2];
cntf[0] = cnt[0];
cntf[1] = cnt[1];
return cntf;
}
protected static int count(final String bam,
protected static int[] count(final String bam,
final Hashtable<String, SAMFileReader> samFileReaderHash,
final String refName,
final int start,
final int end,
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordPredicate samRecordMapQPredicate,
final boolean contained)
final boolean contained,
final boolean byStrand)
{
int cnt = 0;
int cnt[] = new int[2];
cnt[0] = 0;
cnt[1] = 0;
SAMFileReader inputSam = samFileReaderHash.get(bam);
final CloseableIterator<SAMRecord> it = inputSam.query(refName, start, end, contained);
......@@ -141,7 +151,10 @@ class BamUtils
if(samRecordMapQPredicate == null ||
samRecordMapQPredicate.testPredicate(samRecord))
{
cnt++;
if(byStrand && samRecord.getReadNegativeStrandFlag())
cnt[1]++;
else
cnt[0]++;
}
}
}
......@@ -171,8 +184,6 @@ class BamUtils
final SAMRecordPredicate samRecordFlagPredicate,
final SAMRecordPredicate samRecordMapQPredicate)
{
SAMFileReader inputSam = samFileReaderHash.get(bamFile);
final CloseableIterator<SAMRecord> it =
inputSam.query(refName, start, end, false);
......
uk/ac/sanger/artemis/components/alignment/MappedReads.java
+ 96
− 20
View file @ d5fdac2c
......@@ -6,7 +6,7 @@ import java.awt.Point;
import java.awt.Toolkit;
import java.io.File;
import java.text.DecimalFormat;
import java.util.Arrays;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
......@@ -265,10 +265,10 @@ public class MappedReads
class CalculateMappedReads extends SwingWorker
{
Hashtable<String, List<Float>> featureReadCount;
Hashtable<String, List<ReadCount>> featureReadCount;
public Object construct()
{
featureReadCount = new Hashtable<String, List<Float>>();
featureReadCount = new Hashtable<String, List<ReadCount>>();
for (int i = 0; i < features.size(); i++)
{
Feature f = features.elementAt(i);
......@@ -277,21 +277,25 @@ public class MappedReads
int start = f.getRawFirstBase();
int end = f.getRawLastBase();
float fLen = BamUtils.getFeatureLength(f);
List<Float> sampleCounts = new Vector<Float>();
List<ReadCount> sampleCounts = new Vector<ReadCount>();
for (int j = 0; j < bamList.size(); j++)
{
String bam = bamList.get(j);
float cnt = 0;
float cnt[] = new float[2];
if (!useIntrons && f.getSegments().size() > 1)
{
for (int k = 0; k < f.getSegments().size(); k++)
{
start = f.getSegments().elementAt(k).getRawRange().getStart();
end = f.getSegments().elementAt(k).getRawRange().getEnd();
cnt += BamUtils.getCount(start, end, bam, refName, samFileReaderHash,
float tmpcnt[] = new float[2];
tmpcnt = BamUtils.getCount(start, end, bam, refName, samFileReaderHash,
seqNames, offsetLengths, concatSequences, seqLengths,
samRecordFlagPredicate, samRecordMapQPredicate, contained);
cnt[0] += tmpcnt[0];
cnt[1] += tmpcnt[1];
}
}
else
......@@ -300,40 +304,76 @@ public class MappedReads
samRecordFlagPredicate, samRecordMapQPredicate, contained);
if (mappedReads != null)
cnt = (cnt / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
{
cnt[0] = (cnt[0] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
cnt[1] = (cnt[1] / (((float) mappedReads[j] / 1000000.f) * (fLen / 1000.f)));
}
sampleCounts.add(cnt);
sampleCounts.add( new ReadCount(cnt, f.isForwardFeature()) );
}
featureReadCount.put(ReadCountDialog.getFeatureName(f), sampleCounts);
}
return null;
}
public void finished()
{
DecimalFormat df = new DecimalFormat("0.00##");
final DecimalFormat df;
if(mappedReads != null)
df = new DecimalFormat("0.000");
else
df = new DecimalFormat("0");
StringBuffer buff = new StringBuffer();
for (int j = 0; j < bamList.size(); j++)
{
String bam = bamList.get(j);
buff.append("#BAM: " + bam);
if (mappedReads != null)
{
final DecimalFormat df2 = new DecimalFormat("0.000000");
buff.append(" Mapped Reads/million: "
+ df.format(((float) mappedReads[j]) / 1000000.f));
+ df2.format(((float) mappedReads[j]) / 1000000.f));
}
buff.append("\n");
}
buff.append("\n");
Object[] readKey = featureReadCount.keySet().toArray();
Arrays.sort(readKey);
for (Object fId : readKey)
Enumeration<String> enumFeat = featureReadCount.keys();
int n = 0;
while (enumFeat.hasMoreElements())
{
String fId = enumFeat.nextElement();
if(n == 0)
{
for (int i = 0; i < ((String)fId).length(); i++)
buff.append(" ");
buff.append("\t");
for (int j = 0; j < bamList.size(); j++)
{
if(mappedReads != null)
buff.append(" Sense Antisense Total\t");
else
buff.append(" Sense Antisense Total\t");
}
buff.append("\n");
}
buff.append(fId + "\t");
List<Float> cnts = featureReadCount.get(fId);
for (int i = 0; i < cnts.size(); i++)
buff.append(df.format(cnts.get(i)) + (i < cnts.size() - 1 ? "\t" : ""));
List<ReadCount> cnts = featureReadCount.get(fId);
for (ReadCount c: cnts)
{
pad(buff, c.senseCnt, df);
buff.append(" ");
pad(buff, c.antiCnt, df);
buff.append(" ");
pad(buff, c.senseCnt+c.antiCnt, df);
buff.append("\t");
}
buff.append("\n");
n++;
}
FileViewer viewer;
......@@ -347,6 +387,23 @@ public class MappedReads
}
}
private static void pad(StringBuffer buff, float f, final DecimalFormat df)
{
if(f < 10)
buff.append(" ");
else if(f < 100)
buff.append(" ");
else if(f < 1000)
buff.append(" ");
else if(f < 10000)
buff.append(" ");
else if(f < 100000)
buff.append(" ");
else if(f < 1000000)
buff.append(" ");
buff.append(df.format(f));
}
class CalculateTotalMappedReads extends SwingWorker
{
private boolean useAllRefSeqs;
......@@ -417,7 +474,7 @@ public class MappedReads
mappedReads[j] += BamUtils.count(bam, samFileReaderHash, name,
thisStart, thisEnd, samRecordFlagPredicate,
samRecordMapQPredicate, contained);
samRecordMapQPredicate, contained, false)[0];
}
lastLen = len;
......@@ -427,7 +484,7 @@ public class MappedReads
{
mappedReads[j] += BamUtils.count(bam, samFileReaderHash, refName, sbegc,
sendc, samRecordFlagPredicate, samRecordMapQPredicate,
contained);
contained, false)[0];
}
}
}
......@@ -761,4 +818,23 @@ public class MappedReads
dialog.dispose();
}
}
class ReadCount
{
private float senseCnt = 0;
private float antiCnt = 0;
ReadCount(float[] cnt, boolean isFwd)
{
if(isFwd)
{
senseCnt = cnt[0];
antiCnt = cnt[1];
}
else
{
senseCnt = cnt[1];
antiCnt = cnt[0];
}
}
}
}
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