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Bug fixes and improvements to CoverageHistogram. Now displays the frequency of the bin. Also correctly prints out the last element in the coverage histogram (<= vs. <) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1284 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-21 11:55:05 +00:00
parent f13a1e8591
commit 7e04313b4e
1 changed files with 8 additions and 7 deletions
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15
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageHistogram.java
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@ -29,7 +29,7 @@ public class CoverageHistogram extends LocusWalker<Integer,Integer>
//@Argument(fullName="start", shortName="start", required=false, doc="start") public Integer START = 0; //@Argument(fullName="start", shortName="start", required=false, doc="start") public Integer START = 0;
// Private state. // Private state.
int[] coverage_hist; long[] coverage_hist;
int max_depth; int max_depth;
long sum_coverage; long sum_coverage;
@ -39,7 +39,8 @@ public class CoverageHistogram extends LocusWalker<Integer,Integer>
// Walker Interface Functions // Walker Interface Functions
public void initialize() public void initialize()
{ {
coverage_hist = new int[1000000]; coverage_hist = new long[1000000];
Arrays.fill(coverage_hist, 0);
max_depth = 0; max_depth = 0;
sum_coverage = 0; sum_coverage = 0;
@ -62,13 +63,13 @@ public class CoverageHistogram extends LocusWalker<Integer,Integer>
public void onTraversalDone(Integer sum) public void onTraversalDone(Integer sum)
{ {
double mean_coverage = (double)sum_coverage / (double)num_sites; double mean_coverage = (double)sum_coverage / (double)num_sites;
out.printf("# all_sites : mean:%f num_sites:%d\n\n", mean_coverage, num_sites); out.printf("# all_sites : mean:%f num_sites:%d%n", mean_coverage, num_sites);
out.printf("# sites with at least 1 read : mean:%f num_sites:%d\n\n", sum_coverage / ((double)(num_sites - coverage_hist[0])), num_sites - coverage_hist[0]); out.printf("# sites with at least 1 read : mean:%f num_sites:%d%n%n", sum_coverage / ((double)(num_sites - coverage_hist[0])), num_sites - coverage_hist[0]);
out.println("depth count"); out.println("depth count freq");
for (int i = 0; i < max_depth; i++) for (int i = 0; i <= max_depth; i++)
{ {
out.printf("%d %d\n", i, coverage_hist[i]); out.printf("%d %d %f\n", i, coverage_hist[i], (100.0*coverage_hist[i]) / num_sites);
} }
return; return;
} }