[med-svn] [Git][med-team/last-align][master] 5 commits: Packaging update (routine-update)
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Aug 7 04:15:40 BST 2026
Charles Plessy pushed to branch master at Debian Med / last-align
Commits:
419bce64 by Charles Plessy at 2026-08-07T11:16:26+09:00
Packaging update (routine-update)
- - - - -
dd3dd35e by Charles Plessy at 2026-08-07T11:16:43+09:00
New upstream version
- - - - -
439111ff by Charles Plessy at 2026-08-07T11:16:45+09:00
New upstream version 1654
- - - - -
cb96c8fe by Charles Plessy at 2026-08-07T11:16:47+09:00
Update upstream source from tag 'upstream/1654'
Update to upstream version '1654'
with Debian dir 31cb5d2840f852439dee1ba702b44926006f91fd
- - - - -
03e2b495 by Charles Plessy at 2026-08-07T11:35:50+09:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- bin/maf-convert
- debian/changelog
- 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]
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+last-align (1654-1) unstable; urgency=medium
+
+ * Packaging update (routine-update)
+ * New upstream version
+
+ -- Charles Plessy <plessy at debian.org> Fri, 07 Aug 2026 11:21:34 +0900
+
last-align (1652-1) unstable; urgency=medium
* New upstream version
=====================================
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/-/compare/d49d14d89495b52b89f7a60b80ec9a2fe4448b6e...03e2b495b73e593902910e9f84e0ca07070d2834
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/d49d14d89495b52b89f7a60b80ec9a2fe4448b6e...03e2b495b73e593902910e9f84e0ca07070d2834
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