[med-svn] [Git][med-team/bbmap][upstream] New upstream version 38.96+dfsg

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch upstream at Debian Med / bbmap


Commits:
d4520373 by Étienne Mollier at 2022-03-05T12:35:43+01:00
New upstream version 38.96+dfsg
- - - - -


5 changed files:

- README.md
- bbmap.sh
- current/align2/AbstractMapThread.java
- current/shared/Shared.java
- current/stream/ReadStreamByteWriter.java


Changes:

=====================================
README.md
=====================================
@@ -3,4 +3,4 @@
 # Language: Java, Bash
 # Information about documentation is in /docs/readme.txt.
 
-# Version 38.95
+# Version 38.96


=====================================
bbmap.sh
=====================================
@@ -4,7 +4,7 @@ usage(){
 echo "
 BBMap
 Written by Brian Bushnell, from Dec. 2010 - present
-Last modified February 13, 2020
+Last modified February 24, 2022
 
 Description:  Fast and accurate splice-aware read aligner.
 Please read bbmap/docs/guides/BBMapGuide.txt for more information.


=====================================
current/align2/AbstractMapThread.java
=====================================
@@ -970,7 +970,6 @@ public abstract class AbstractMapThread extends Thread {
 			}
 		}
 		
-		
 		final SiteScore ss=r.topSite();
 		assert(ss==r.topSite());
 		
@@ -1343,11 +1342,14 @@ public abstract class AbstractMapThread extends Thread {
 		if(!printSecondary || r.numSites()<2){return;}
 		int max=r.topSite().slowScore;
 		int min=Tools.min(max-500, (int)(max*SECONDARY_SITE_SCORE_RATIO));
+		
 		if(r.ambiguous()){//Ensures ambiguous reads will have at least one secondary site
-			min=Tools.max(min, r.sites.get(1).score);
+			min=Tools.min(min, r.sites.get(1).slowScore);
 		}
 		for(int i=r.sites.size()-1; i>0; i--){
-			if(r.sites.get(i).slowScore<min){r.sites.remove(i);}
+			if(r.sites.get(i).slowScore<min){//Fixed: max -> min, score -> slowscore
+				r.sites.remove(i);
+			}
 		}
 //		assert(false) : r.mapScore+", "+max+", "+cap+", "+r.list;
 //		assert(r.list.size()<2) : "\n"+max+", "+min+", "+r.list+"\n";


=====================================
current/shared/Shared.java
=====================================
@@ -125,8 +125,8 @@ public class Shared {
 	public static final int GAPCOST=Tools.max(1, GAPLEN/64);
 	public static final byte GAPC='-';
 	
-	public static String BBMAP_VERSION_STRING="38.95";
-	public static String BBMAP_VERSION_NAME="CFS Migration";
+	public static String BBMAP_VERSION_STRING="38.96";
+	public static String BBMAP_VERSION_NAME="Return True";
 	
 	public static boolean TRIM_READ_COMMENTS=false;
 	public static boolean TRIM_RNAME=false; //For mapped sam reads


=====================================
current/stream/ReadStreamByteWriter.java
=====================================
@@ -574,6 +574,8 @@ public class ReadStreamByteWriter extends ReadStreamWriter {
 			SamLine sl1=(r==null ? null : (USE_ATTACHED_SAMLINE && r.samline!=null ? r.samline : new SamLine(r, 0)));
 			SamLine sl2=(r2==null ? null : (USE_ATTACHED_SAMLINE && r2.samline!=null ? r2.samline : new SamLine(r2, 1)));
 
+//			assert(false) : OUTPUT_SAM_SECONDARY_ALIGNMENTS+", "+r.numSites()+", "+r.sites;
+			
 			if(r!=null){
 				
 				if(verbose && r.numSites()>0){
@@ -640,7 +642,7 @@ public class ReadStreamByteWriter extends ReadStreamWriter {
 						clone.setFromSite(ss);
 						clone.setSecondary(true);
 //						assert(false) : r.mapScore+"\n"+ss.header()+"\n"+r.list+"\n";
-						SamLine sl=new SamLine(clone, 0);
+						SamLine sl=new SamLine(clone, 1);
 						assert(!sl.primary());
 //						sl.setPrimary(false);
 						



View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d

-- 
View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/d4520373ab54d86278cb3713e4addaba8d2d8f0d
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