Étienne Mollier pushed to branch master at Debian Med / bbmap
Commits:
7fc55fd6 by Étienne Mollier at 2022-03-05T12:35:42+01:00
routine-update: New upstream version
- - - - -
d4520373 by Étienne Mollier at 2022-03-05T12:35:43+01:00
New upstream version 38.96+dfsg
- - - - -
05a45e9d by Étienne Mollier at 2022-03-05T12:35:51+01:00
Update upstream source from tag 'upstream/38.96+dfsg'
Update to upstream version '38.96+dfsg'
with Debian dir 6e0619020bd2d499f14f3e5515f89841f3b222df
- - - - -
aacc1c2a by Étienne Mollier at 2022-03-05T12:46:55+01:00
Add cppflags.patch: append CPPFLAGS to build flags
This enables fortifying the source.
- - - - -
f01a0026 by Étienne Mollier at 2022-03-05T12:48:57+01:00
ready changelog to upload to unstable
- - - - -
8 changed files:
- README.md
- bbmap.sh
- current/align2/AbstractMapThread.java
- current/shared/Shared.java
- current/stream/ReadStreamByteWriter.java
- debian/changelog
- + debian/patches/cppflags.patch
- debian/patches/series
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);
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+bbmap (38.96+dfsg-1) unstable; urgency=medium
+
+ * New upstream version
+ * Add cppflags.patch: append CPPFLAGS to build flags; this enables fortifying
+ the source.
+
+ -- Étienne Mollier <[email protected]> Sat, 05 Mar 2022 12:48:46 +0100
+
bbmap (38.95+dfsg-1) unstable; urgency=medium
* New upstream version
=====================================
debian/patches/cppflags.patch
=====================================
@@ -0,0 +1,17 @@
+Description: add CPPFLAGS build options to support fortify source
+Author: Étienne Mollier <[email protected]>
+Forwarded: not-needed
+Last-Update: 2022-03-05
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bbmap.orig/jni/makefile.linux
++++ bbmap/jni/makefile.linux
+@@ -5,7 +5,7 @@
+ OBJ=BandedAlignerJNI.o MultiStateAligner11tsJNI.o BBMergeOverlapper.o
IceCreamAlignerJNI.o
+
+ %.o: %.c
+- $(CC) $(CFLAGS) $(INCS) -c -o $@ $<
++ $(CC) $(CPPFLAGS) $(CFLAGS) $(INCS) -c -o $@ $<
+
+ libbbtoolsjni.so: $(OBJ)
+ $(CC) -o $@ $^ $(LDFLAGS)
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
debug_symbols.patch
32bit.patch
+cppflags.patch
View it on GitLab:
https://salsa.debian.org/med-team/bbmap/-/compare/be0820897d8f69848b09def8c4319febddee7691...f01a00267ac54822b12ad0234e35849822af8180
--
View it on GitLab:
https://salsa.debian.org/med-team/bbmap/-/compare/be0820897d8f69848b09def8c4319febddee7691...f01a00267ac54822b12ad0234e35849822af8180
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