[med-svn] [Git][med-team/last-align][master] 7 commits: New upstream version
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Fri Jul 10 04:34:56 BST 2026
Charles Plessy pushed to branch master at Debian Med / last-align
Commits:
8048e741 by Charles Plessy at 2026-07-10T12:06:20+09:00
New upstream version
- - - - -
2f174580 by Charles Plessy at 2026-07-10T12:06:21+09:00
New upstream version 1652
- - - - -
9dc8dcee by Charles Plessy at 2026-07-10T12:06:22+09:00
Update upstream source from tag 'upstream/1652'
Update to upstream version '1652'
with Debian dir 25872f29c85879a8785e12d76564ff821d8e9703
- - - - -
1bdabc15 by Charles Plessy at 2026-07-10T12:06:23+09:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
ab4345fd by Charles Plessy at 2026-07-10T12:06:46+09:00
Changes made by cme
- - - - -
e11531ec by Charles Plessy at 2026-07-10T12:06:59+09:00
Reformat the Last-Update date as ISO YYYY-MM-DD.
Changes-By: lintian-brush
Fixes: lintian: source: invalid-dep3-format-patch-wrong-last-update [debian/patches/helpMakefiles.patch]
See-also: https://lintian.debian.org/tags/invalid-dep3-format-patch-wrong-last-update.html
- - - - -
d49d14d8 by Charles Plessy at 2026-07-10T12:14:42+09:00
routine-update: Ready to upload to unstable
- - - - -
7 changed files:
- bin/maf-convert
- debian/changelog
- debian/control
- debian/patches/helpMakefiles.patch
- src/makefile
- test/maf-convert-test.out
- test/maf-convert-test.sh
Changes:
=====================================
bin/maf-convert
=====================================
@@ -1076,11 +1076,20 @@ def writeBlastTab(opts, formatName, geneticCode, maf):
gapOpens, begB, endB, begA, endA]
score, evalue = scoreAndEvalue(aLine)
+
+ bitScore = None
+ if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
+ bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
+ bitScore = "%.3g" % bitScore
+
+ if formatName == "blasttab+":
+ if not evalue: evalue = 'NA'
+ if not bitScore: bitScore = 'NA'
+
if evalue:
out.append(evalue)
- if score and opts.bitScoreA is not None and opts.bitScoreB is not None:
- bitScore = opts.bitScoreA * float(score) - opts.bitScoreB
- out.append("%.3g" % bitScore)
+ if bitScore:
+ out.append(bitScore)
if formatName == "blasttab+":
out += [seqLenB, seqLenA, score]
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+last-align (1652-1) unstable; urgency=medium
+
+ * New upstream version
+ * Standards-Version: 4.7.4 (routine-update)
+ * Reflow Uploaders field (cme)
+ * Reformat the Last-Update date as ISO YYYY-MM-DD.
+
+ -- Charles Plessy <plessy at debian.org> Fri, 10 Jul 2026 12:11:37 +0900
+
last-align (1651-2) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,27 +1,32 @@
Source: last-align
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>
+Uploaders:
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>,
Section: science
-Build-Depends: debhelper-compat (= 13),
- help2man,
- python3-pil,
- zlib1g-dev,
- libsimde-dev,
- architecture-is-64-bit
-Standards-Version: 4.7.3
+Build-Depends:
+ debhelper-compat (= 14),
+ help2man,
+ python3-pil,
+ zlib1g-dev,
+ libsimde-dev,
+ architecture-is-64-bit,
Vcs-Browser: https://salsa.debian.org/med-team/last-align
Vcs-Git: https://salsa.debian.org/med-team/last-align.git
Homepage: https://gitlab.com/mcfrith/last
Package: last-align
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- python3
-Recommends: python3-pil,
- parallel
-Built-Using: ${Built-Using}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ python3,
+Recommends:
+ python3-pil,
+ parallel,
+Built-Using:
+ ${Built-Using},
Description: genome-scale comparison of biological sequences
LAST is software for comparing and aligning sequences, typically DNA or
protein sequences. LAST is similar to BLAST, but it copes better with very
=====================================
debian/patches/helpMakefiles.patch
=====================================
@@ -1,6 +1,6 @@
Author: Steffen Moeller,
Nilesh Patra
-Last-Update: 2021-04-19 17:37:27 +0530
+Last-Update: 2021-04-19
Description: Propagate variables to Makefile
--- a/src/makefile
=====================================
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: 1651) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1652) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
test/maf-convert-test.out
=====================================
@@ -8349,6 +8349,9 @@ chrUn_KI270748v1 UN-L1PA2_pol#LINE/L1 93.39 227 15 0 3860 4540 1049 1275 1.5e-16
chrUn_KI270748v1 UN-L1MA6_pol#LINE/L1 62.18 386 107 14 3661 2577 518 879 2.5e-152 546 93321 1275 1607.4
chrUn_KI270748v1 UN-L1MA6_pol#LINE/L1 61.64 292 89 8 90089 89272 884 1164 2e-147 530 93321 1275 1559.7
chrUn_KI270748v1 UN-L1PA16_pol#LINE/L1 64.07 359 96 11 17572 18588 527 864 3.8e-142 512 93321 1276 1508.0
+90089 chrX 92.38 656 8 21 49 670 23075590 23076237 NA NA 2478 156040895 3061
+90089 chr7 87.72 114 1 6 776 676 121351143 121351256 NA NA 2478 159345973 493
+90089 chr7 96.82 1699 8 33 2431 777 121348854 121350550 NA NA 2478 159345973 9115
UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 63.82 633 194 13 658 1273 13905 15715 0 1.08e+03
UN-L1PA2_pol#LINE/L1 chrUn_KI270748v1 93.39 227 15 0 1049 1275 3860 4540 1.5e-169 603
UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 62.18 386 107 14 518 879 3661 2577 2.5e-152 546
=====================================
test/maf-convert-test.sh
=====================================
@@ -25,6 +25,7 @@ maf2=bs100.maf
$r -l120 blast HERVS71A.maf # test ambiguous N bases
$r blasttab $maf2
$r blasttab+ frameshift-new.maf
+ $r blasttab+ 90089.maf
$r -s2 blasttab frameshift-new.maf
maf-cut DF0000170.5:633-798 herv30.maf | $r blasttab # gaps at edges
maf-cut DF0000170.5:633-798 herv30.maf | $r -s2 blasttab # gaps at edges
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/55b22d33fc6802947099ccec2cd4aeb65a32e3a4...d49d14d89495b52b89f7a60b80ec9a2fe4448b6e
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/55b22d33fc6802947099ccec2cd4aeb65a32e3a4...d49d14d89495b52b89f7a60b80ec9a2fe4448b6e
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