zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Shame on us. FlagStat used ints instead of longs, so we ended up getting negative read counts 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4022 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-13 03:00:57 +00:00
parent 71c4d3f33d
commit f874e548aa
1 changed files with 15 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

36
java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java
View File

@ -43,18 +43,18 @@ import java.text.NumberFormat;
public class FlagStatWalker extends ReadWalker<Integer, Integer> { public class FlagStatWalker extends ReadWalker<Integer, Integer> {
// what comes out of the flagstat // what comes out of the flagstat
static class FlagStat { static class FlagStat {
int readCount = 0; long readCount = 0L;
int QC_failure = 0; long QC_failure = 0L;
int duplicates = 0; long duplicates = 0L;
int mapped = 0; long mapped = 0L;
int paired_in_sequencing = 0; long paired_in_sequencing = 0L;
int read1 = 0; long read1 = 0L;
int read2 = 0; long read2 = 0L;
int properly_paired = 0; long properly_paired = 0L;
int with_itself_and_mate_mapped = 0; long with_itself_and_mate_mapped = 0L;
int singletons = 0; long singletons = 0L;
int with_mate_mapped_to_a_different_chr = 0; long with_mate_mapped_to_a_different_chr = 0L;
int with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5 = 0; long with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5 = 0L;
public String toString() { public String toString() {
String ret = ""; String ret = "";
@ -155,21 +155,15 @@ public class FlagStatWalker extends ReadWalker<Integer, Integer> {
} }
public Integer reduceInit public Integer reduceInit() {
() {
return 0; return 0;
} }
public Integer reduce public Integer reduce(Integer value, Integer sum) {
( Integer
value, Integer
sum ) {
return value + sum; return value + sum;
} }
public void onTraversalDone public void onTraversalDone(Integer result) {
( Integer
result ) {
//out.println("[REDUCE RESULT] Traversal result is: " + result); //out.println("[REDUCE RESULT] Traversal result is: " + result);
out.println(myStat.toString()); out.println(myStat.toString());
} }