[med-svn] [Git][med-team/bbmap][master] 3 commits: Fixing some syntax issues in (probably) useless code portions

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / bbmap


Commits:
7404c092 by Pierre Gruet at 2023-10-19T22:20:23+02:00
Fixing some syntax issues in (probably) useless code portions

- - - - -
79862782 by Pierre Gruet at 2023-10-19T22:23:04+02:00
Updating changelog

- - - - -
1b61c58e by Pierre Gruet at 2023-10-19T22:23:12+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/java_syntax.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,13 @@
-bbmap (39.03+dfsg-1) UNRELEASED; urgency=medium
+bbmap (39.03+dfsg-1) unstable; urgency=medium
 
+  * Team upload
+  * Fixing some syntax issues linked to seemingly old, unused code
+
+  [ Andreas Tille ]
   * New upstream version
   * Standards-Version: 4.6.2 (routine-update)
 
- -- Andreas Tille <tille at debian.org>  Wed, 18 Oct 2023 15:09:52 +0200
+ -- Pierre Gruet <pgt at debian.org>  Thu, 19 Oct 2023 22:23:06 +0200
 
 bbmap (39.01+dfsg-3) unstable; urgency=medium
 


=====================================
debian/patches/java_syntax.patch
=====================================
@@ -0,0 +1,33 @@
+Description: fixing syntax issues in (probably) unused classes
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: https://sourceforge.net/p/bbmap/tickets/60/
+Last-Update: 2023-10-19
+
+--- a/current/jgi/RepeatFinder.java
++++ b/current/jgi/RepeatFinder.java
+@@ -509,7 +509,7 @@
+ 	}
+ 	
+ 	final int maskRepeat(CRange r) {
+-		return maskRepeat(((Read)r.o).bases, r.a, r.b);
++		return maskRepeat(((Read)r.obj).bases, r.a, r.b);
+ 	}
+ 	
+ 	final int maskRepeat(byte[] bases, int start, int stop) {
+--- a/current/structures/SeqMap.java
++++ b/current/structures/SeqMap.java
+@@ -254,6 +254,14 @@
+ 		return max;
+ 	}
+ 	
++	public static SeqMap load(String ref, int k, int mm, int minCount, boolean rcomp) {
++        return load(ref, k, mm, minCount, rcomp, null);
++    }
++
++	public static SeqMap load(ArrayList<Read> reads, int k, int mm, int minCount, boolean rcomp) {
++        return load(reads, k, mm, minCount, rcomp, null);
++    }
++
+ 	public static SeqMap load(String ref, int k, int mm, int minCount, boolean rcomp, CellNet net) {
+ 		ArrayList<Read> reads=FastaReadInputStream.toReads(ref, FileFormat.FASTA, -1);
+ 		return load(reads, k, mm, minCount, rcomp, net);


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 debug_symbols.patch
 32bit.patch
 cppflags.patch
+java_syntax.patch



View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/compare/ba797500e1e46f1ea218b5538b8f584c16e69b44...1b61c58e6d914cfc5d8a7b7a50bd59c172b680b4

-- 
View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/compare/ba797500e1e46f1ea218b5538b8f584c16e69b44...1b61c58e6d914cfc5d8a7b7a50bd59c172b680b4
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