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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