[med-svn] [Git][med-team/last-align][upstream] New upstream version 1654

[Charles Plessy (@plessy)]

Charles Plessy pushed to branch upstream at Debian Med / last-align


Commits:
439111ff by Charles Plessy at 2026-08-07T11:16:45+09:00
New upstream version 1654
- - - - -


6 changed files:

- bin/maf-convert
- src/makefile
- src/tantan.cc
- + test/empty-aln.maf
- test/maf-convert-test.out
- test/maf-convert-test.sh


Changes:

=====================================
bin/maf-convert
=====================================
@@ -180,7 +180,9 @@ def mafInput(opts, lines):
     pLines = []
     for line in lines:
         if line[0] == "s":
-            junk, seqName, beg, span, strand, seqLen, row = line.split()
+            fields = line.split()
+            seqName, beg, span, strand, seqLen = fields[1:6]
+            row = fields[6] if len(fields) > 6 else ""
             beg = int(beg)
             span = int(span)
             seqLen = int(seqLen)
@@ -956,7 +958,8 @@ def writeBlast(opts, geneticCode, codon2triplet, maf, oldQueryName):
         alnSize = len(sySeq)
         lineSize = opts.linesize
 
-    matchPercent = 100 * matches // alnSize  # round down, like BLAST
+    # round down, like BLAST
+    matchPercent = 100 * matches // alnSize if alnSize else 0
     identLine = " Identities = %s/%s (%s%%)" % (matches, alnSize, matchPercent)
     if gaps:
         gapPercent = 100 * gaps // alnSize  # round down, like BLAST
@@ -1070,7 +1073,7 @@ def writeBlastTab(opts, formatName, geneticCode, maf):
         matches = sum(x == y for x, y in alignmentColumns)
         mismatches = alnSize - matches - rowA.count("-") - rowB.count("-")
 
-    matchPercent = "%.2f" % (100.0 * matches / alnSize)
+    matchPercent = "%.2f" % (100.0 * matches / alnSize) if alnSize else 'NA'
 
     out = [seqNameB, seqNameA, matchPercent, alnSize, mismatches,
            gapOpens, begB, endB, begA, endA]


=====================================
src/makefile
=====================================
@@ -95,7 +95,7 @@ ScoreMatrixData.hh: ../data/*.mat
 	../build/mat-inc.sh ../data/*.mat > $@
 
 VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1652) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1654) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
 
 VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
 


=====================================
src/tantan.cc
=====================================
@@ -425,13 +425,14 @@ struct Tantan {
     }
 
     double z = forwardTotal();
+    double zInv = 1 / z;
 
     initializeBackwardAlgorithm();
 
     while (seqPtr > seqBeg) {
       --seqPtr;
       --letterProbs;
-      double nonRepeatProb = *letterProbs * backgroundProb / z;
+      double nonRepeatProb = *letterProbs * backgroundProb * zInv;
       // Convert nonRepeatProb to a float, so that it is more likely
       // to be exactly 1 when it should be, e.g. for the 1st letter of
       // a sequence:


=====================================
test/empty-aln.maf
=====================================
@@ -0,0 +1,4 @@
+a score=27.9 E=0.018 anchor=94,498
+s ABC2_membrane_3  94 0 +  346 
+s decoy280863     498 0 + 2612 
+P                              


=====================================
test/maf-convert-test.out
=====================================
@@ -24253,3 +24253,14 @@ NC_077230.1	0	chr1	403534	0	104187276H10=1X2=1X3=1X3=1I3=1X10=1X6=4X1=1X1=2X1=1X
 1607.4	UN-L1MA6_pol#LINE/L1	517	362	+	1275	chrUn_KI270748v1	89660	1085	-	93321	10,1:2,16,0:2,12,1:2,5,1:2,4,3:1,8,1:0,13,1:0,92,1:1,15,2:0,35,1:1,11,1:1,14,0:30,24,1:1,80,1:1,8	EG2=5e-147	E=2.5e-152
 1559.7	UN-L1MA6_pol#LINE/L1	883	281	+	1275	chrUn_KI270748v1	3232	818	-	93321	7,1:2,33,1:1,40,1:1,84,4:2,4,3:0,44,0:1,37,1:2,12,1:2,8	EG2=3.8e-142	E=2e-147
 1508.0	UN-L1PA16_pol#LINE/L1	526	338	+	1276	chrUn_KI270748v1	17571	1017	+	93321	102,1:0,63,1:0,21,1:0,18,2:2,14,0:29,14,3:2,6,1:1,38,1:1,7,1:2,22,1:1,8,0:1,13	EG2=7.4e-137	E=3.8e-142
+decoy280863	ABC2_membrane_3	NA	0	0	0	499	498	95	94	0.018	NA	2612	346	27.9
+Query= decoy280863
+         (2612 letters)
+
+>ABC2_membrane_3
+          Length = 346
+
+ Score = 27.9, Expect = 0.018
+ Identities = 0/0 (0%)
+ Strand = Plus / Plus
+


=====================================
test/maf-convert-test.sh
=====================================
@@ -56,4 +56,6 @@ maf2=bs100.maf
     head -n999 $maf1 | $r -n tab
     head -n999 $maf1 | $r tab
     $r -n tab frameshift-new.maf
+    $r blasttab+ empty-aln.maf
+    $r blast empty-aln.maf
 } | diff -u maf-convert-test.out -



View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/439111ffef1a0e271e71216935511a58fd90e0ed

-- 
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/439111ffef1a0e271e71216935511a58fd90e0ed
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