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bug fixes for scoring and summit reporting
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evantarbell committed Jan 31, 2019
1 parent 83fe5d2 commit a5433f7
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Showing 2 changed files with 7 additions and 5 deletions.
9 changes: 5 additions & 4 deletions src/HMMR_ATAC/Main_HMMR_Driver.java
Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,7 @@ public class Main_HMMR_Driver {
/*
* Version number. Change as needed
*/
private static String versionNum = "1.2.2";
private static String versionNum = "1.2.3";

@SuppressWarnings("unchecked")
public static void main(String[] args) throws IOException {
Expand Down Expand Up @@ -505,7 +505,9 @@ public static void main(String[] args) throws IOException {
}
}
//out.close();
NFR.close();MONO.close();DI.close();TRI.close();
if(printHMMRTracks){
NFR.close();MONO.close();DI.close();TRI.close();
}
/**
* Report the final results as peaks, bedgraphs and summits, if desired
*/
Expand Down Expand Up @@ -602,8 +604,7 @@ public static void main(String[] args) throws IOException {
if (peaks && (int) temp.getScore2() == peak
&& temp.getLength() >= minLength) {
if (temp.getSummit() != null) {
summits.println(temp.getSummit()
.toString_ScoredSummit());
summits.println(temp.toString_ScoredSummit());
}
pks.println(temp.toString_gappedPeak());
}
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3 changes: 2 additions & 1 deletion src/Node/TagNode.java
Original file line number Diff line number Diff line change
Expand Up @@ -166,7 +166,8 @@ public String toString_ScoredBdg(){
* @return a String representing the scored summit entry
*/
public String toString_ScoredSummit(){
String ans = CHROM+"\t"+BP_START+"\t"+BP_STOP+"\t"+uniqID+"\t"+score3;

String ans = CHROM+"\t"+this.getSummit().getStart()+"\t"+this.getSummit().getStop()+"\t"+uniqID+"\t"+score3;
return ans;
}
/**
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