diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java index 27298c4ed..1a6ffd09d 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/FlagStatWalker.java @@ -43,18 +43,18 @@ import java.text.NumberFormat; public class FlagStatWalker extends ReadWalker { // what comes out of the flagstat static class FlagStat { - int readCount = 0; - int QC_failure = 0; - int duplicates = 0; - int mapped = 0; - int paired_in_sequencing = 0; - int read1 = 0; - int read2 = 0; - int properly_paired = 0; - int with_itself_and_mate_mapped = 0; - int singletons = 0; - int with_mate_mapped_to_a_different_chr = 0; - int with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5 = 0; + long readCount = 0L; + long QC_failure = 0L; + long duplicates = 0L; + long mapped = 0L; + long paired_in_sequencing = 0L; + long read1 = 0L; + long read2 = 0L; + long properly_paired = 0L; + long with_itself_and_mate_mapped = 0L; + long singletons = 0L; + long with_mate_mapped_to_a_different_chr = 0L; + long with_mate_mapped_to_a_different_chr_maq_greaterequal_than_5 = 0L; public String toString() { String ret = ""; @@ -155,21 +155,15 @@ public class FlagStatWalker extends ReadWalker { } - public Integer reduceInit - () { + public Integer reduceInit() { return 0; } - public Integer reduce - ( Integer - value, Integer - sum ) { + public Integer reduce(Integer value, Integer sum) { return value + sum; } - public void onTraversalDone - ( Integer - result ) { + public void onTraversalDone(Integer result) { //out.println("[REDUCE RESULT] Traversal result is: " + result); out.println(myStat.toString()); }