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vast speedup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@729 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-05-16 15:27:58 +00:00
parent 6f1559bd77
commit 947bac5cdc
1 changed files with 18 additions and 12 deletions
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30
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java
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@ -18,17 +18,22 @@ public class CoverageBySample extends LocusWalker<String, String>
public boolean requiresReads() { return true; } public boolean requiresReads() { return true; }
private SAMFileHeader header;
public void initialize() public void initialize()
{ {
GenomeAnalysisEngine toolkit = this.getToolkit(); GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getSamReader().getFileHeader(); this.header = toolkit.getEngine().getSAMHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups(); List<SAMReadGroupRecord> read_groups = header.getReadGroups();
sample_names = new ArrayList<String>(); sample_names = new ArrayList<String>();
HashSet<String> unique_sample_names = new HashSet<String>();
for (int i = 0; i < read_groups.size(); i++) for (int i = 0; i < read_groups.size(); i++)
{ {
String sample_name = read_groups.get(i).getSample(); String sample_name = read_groups.get(i).getSample();
if (unique_sample_names.contains(sample_name)) { continue; }
unique_sample_names.add(sample_name);
sample_names.add(sample_name); sample_names.add(sample_name);
} }
} }
@ -36,30 +41,31 @@ public class CoverageBySample extends LocusWalker<String, String>
public String map(RefMetaDataTracker tracker, char ref, LocusContext context) public String map(RefMetaDataTracker tracker, char ref, LocusContext context)
{ {
String line = context.getLocation().getContig() + " " + context.getLocation().getStart() + " " ; String line = context.getLocation().getContig() + " " + context.getLocation().getStart() + " " ;
HashMap<String,Integer> counts = countReadsBySample(context);
for (int i = 0; i < sample_names.size(); i++) for (int i = 0; i < sample_names.size(); i++)
{ {
int count = countReadsBySample(context, sample_names.get(i)); int count = counts.get(sample_names.get(i));
line += " " + count; line += " " + count;
} }
line += "\n"; line += "\n";
return line; return line;
} }
private int countReadsBySample(LocusContext context, String sample_name) private HashMap<String,Integer> countReadsBySample(LocusContext context)
{ {
int count = 0; HashMap<String,Integer> counts = new HashMap<String,Integer>();
for (int i = 0; i < sample_names.size(); i++)
{
counts.put(sample_names.get(i), 0);
}
for (int i = 0; i < context.getReads().size(); i++) for (int i = 0; i < context.getReads().size(); i++)
{ {
SAMRecord read = context.getReads().get(i); SAMRecord read = context.getReads().get(i);
Integer offset = context.getOffsets().get(i);
String RG = (String)(read.getAttribute("RG")); String RG = (String)(read.getAttribute("RG"));
String sample = read.getHeader().getReadGroup(RG).getSample(); String sample = header.getReadGroup(RG).getSample();
if (sample == sample_name) counts.put(sample, counts.get(sample)+1);
{
count += 1;
}
} }
return count; return counts;
} }
public void onTraversalDone() public void onTraversalDone()
@ -82,7 +88,7 @@ public class CoverageBySample extends LocusWalker<String, String>
public String reduce(String line, String sum) public String reduce(String line, String sum)
{ {
out.print(line); out.print(line);
return sum + line; return "";
} }