[med-svn] [Git][med-team/bbmap][upstream] New upstream version 38.89+dfsg

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / bbmap


Commits:
5521b9ce by Nilesh Patra at 2021-02-01T16:21:55+05:30
New upstream version 38.89+dfsg
- - - - -


4 changed files:

- README.md
- current/dna/AminoAcid.java
- current/shared/Shared.java
- docs/changelog.txt


Changes:

=====================================
README.md
=====================================
@@ -3,4 +3,4 @@
 # Language: Java, Bash
 # Information about documentation is in /docs/readme.txt.
 
-# Version 38.88
+# Version 38.89


=====================================
current/dna/AminoAcid.java
=====================================
@@ -192,7 +192,7 @@ public final class AminoAcid {
 	/** Element i is: 5-bit alphabetical code for a symbol, 0 otherwise */
 	public static final byte[] acidToNumber0=new byte[128];//Rename acidToNumber0
 	
-	/** Element i is: 5-bit alphabetical code for a symbol (plus X and . and -), -1 otherwise */
+	/** Element i is: 5-bit alphabetical code for a symbol (plus X, B, J, Z, . and -), -1 otherwise */
 	public static final byte[] acidToNumberExtended=new byte[128];
 	
 	/** Element i is: 5-bit alphabetical code for a symbol, -1 otherwise */
@@ -891,8 +891,16 @@ public final class AminoAcid {
 		for(int i=0; i<acidToNumber.length; i++){
 			acidToNumberExtended[i]=acidToNumber[i];
 		}
-		acidToNumberExtended['x']=acidToNumberExtended['X']=acidToNumberExtended['.']=(byte)(Tools.max(acidToNumberExtended)+1);
-		acidToNumberExtended['-']=(byte)(Tools.max(acidToNumberExtended)+1);
+		
+		{
+			byte anySym=(byte)(Tools.max(acidToNumberExtended)+1);
+			byte dash=(byte)(anySym+1);
+			acidToNumberExtended['x']=acidToNumberExtended['X']=acidToNumberExtended['.']=anySym;
+			acidToNumberExtended['b']=acidToNumberExtended['B']=anySym;
+			acidToNumberExtended['z']=acidToNumberExtended['Z']=anySym;
+			acidToNumberExtended['j']=acidToNumberExtended['J']=anySym;
+			acidToNumberExtended['-']=dash;
+		}
 		
 		acidToNumber8['H']=acidToNumber8['K']=acidToNumber8['R']=0;
 		acidToNumber8['D']=acidToNumber8['E']=1;


=====================================
current/shared/Shared.java
=====================================
@@ -124,8 +124,8 @@ public class Shared {
 	public static final int GAPCOST=Tools.max(1, GAPLEN/64);
 	public static final byte GAPC='-';
 	
-	public static String BBMAP_VERSION_STRING="38.88";
-	public static String BBMAP_VERSION_NAME="Tree Traversal";
+	public static String BBMAP_VERSION_STRING="38.89";
+	public static String BBMAP_VERSION_NAME="Kmer Sets";
 	
 	public static boolean TRIM_READ_COMMENTS=false;
 	public static boolean TRIM_RNAME=false; //For mapped sam reads


=====================================
docs/changelog.txt
=====================================
@@ -888,6 +888,8 @@ ApplyVariants should correctly handle truncated scaffold names now.
 RQCFilter/ReadStats static variable hangover fixed.
 Wrote KExpand and kmutate.sh for creating sets of mutant kmers.
 Split Parse class off from Tools.
+38.89
+Added support for degenerate amino acid symbols B, J, Z.
 
 
 TODO: Variant whitelist for callvariants



View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/5521b9cea9e7a544325a01572872ec7b88a85b9e

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View it on GitLab: https://salsa.debian.org/med-team/bbmap/-/commit/5521b9cea9e7a544325a01572872ec7b88a85b9e
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