[med-svn] [Git][med-team/staden-io-lib][master] 10 commits: New upstream version 1.15.1
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Feb 22 17:25:29 GMT 2026
Étienne Mollier pushed to branch master at Debian Med / staden-io-lib
Commits:
647d01bd by Étienne Mollier at 2026-02-22T18:03:34+01:00
New upstream version 1.15.1
- - - - -
4bb09fab by Étienne Mollier at 2026-02-22T18:03:49+01:00
Update upstream source from tag 'upstream/1.15.1'
Update to upstream version '1.15.1'
with Debian dir aaf8c712935698586a7a27103c0d6ccacf82827f
- - - - -
022789ca by Étienne Mollier at 2026-02-22T18:04:41+01:00
d/control: drop redundant Priority: optional.
- - - - -
6f57434b by Étienne Mollier at 2026-02-22T18:05:00+01:00
d/control: drop redundant Rules-Requires-Root: no.
- - - - -
ba2716af by Étienne Mollier at 2026-02-22T18:05:29+01:00
d/control: declare compliance to standards version 4.7.3.
- - - - -
69909591 by Étienne Mollier at 2026-02-22T18:07:18+01:00
d/watch: move to uscan v5 Github template.
- - - - -
08fdcefc by Étienne Mollier at 2026-02-22T18:21:48+01:00
d/control: remove version on libstaden-read14 conflict.
- - - - -
1c77b114 by Étienne Mollier at 2026-02-22T18:23:41+01:00
d/libstaden-read14t64.lintian-overrides: remove.
This file held a new ununsed lintian override.
- - - - -
b4cc5ba8 by Étienne Mollier at 2026-02-22T18:24:07+01:00
fix_fseeko.patch: normalize Last-Update timestamp.
- - - - -
8238f2da by Étienne Mollier at 2026-02-22T18:24:57+01:00
d/changelog: ready for upload to unstable.
- - - - -
8 changed files:
- CHANGES
- README.md
- configure.ac
- debian/changelog
- debian/control
- − debian/libstaden-read14t64.lintian-overrides
- debian/patches/fix_fseeko.patch
- debian/watch
Changes:
=====================================
CHANGES
=====================================
@@ -1,3 +1,11 @@
+Version 1.15.1 (14th July 2025)
+--------------
+
+This is simply a change to the build infrastructure, with newer
+versions of the htscodecs submodule and an updated configure/libtool
+script to help MacOS builds.
+
+
Version 1.15.0 (14th April 2023)
--------------
=====================================
README.md
=====================================
@@ -1,4 +1,4 @@
-Io_lib: Version 1.15.0
+Io_lib: Version 1.15.1
=======================
Io_lib is a library of file reading and writing code to provide a general
@@ -33,6 +33,14 @@ See the CHANGES for a summary of older updates or git logs for the
full details.
+Version 1.15.1 (14th July 2025)
+--------------
+
+This is simply a change to the build infrastructure, with newer
+versions of the htscodecs submodule and an updated configure/libtool
+script to help MacOS builds.
+
+
Version 1.15.0 (14th April 2023)
--------------
@@ -98,6 +106,118 @@ CPU running Ubuntu 20.04 under Microsoft's WSL2.
|-V4.0 -X small | 162.3| 34.8| 20.2|rANS++,tok3,fqz |
|-V4.0 -X archive | 157.9| 82.2| 26.2|rANS++,tok3,fqz,bzip2,arith|
+```mermaid
+gantt
+ title 10 million Illumina NovaSeq records
+ todayMarker off
+ dateFormat X
+ axisFormat %s
+
+ section BAM
+ -5 zlib 66s / 6s : 0,518
+ -1, 17s / 3s : 0,584
+ -5, 28s / 3s : 0,525
+ -9, 810s / 3s : 0,486
+ - : 0,0
+
+ section CRAM 2.0
+ fast, 23s / 8s : 0,294
+ normal, 33s / 8s : 0,253
+ small, 85s / 23s : 0,208
+ archive, 88s / 24s : 0,206
+ - : 0,0
+
+ section CRAM 3.0
+ fast, 20s / 8s : 0,241
+ normal, 23s / 9s : 0,208
+ small, 60s / 14s : 0,202
+ archive, 62s / 14s : 0,200
+ - : 0,0
+
+ section CRAM 3.1
+ fast, 22s / 8s : 0,237
+ normal, 27s / 9s : 0,176
+ small, 48s / 25s : 0,167
+ archive, 72s / 21s : 0,162
+ - : 0,0
+
+ section CRAM 4.0
+ fast, 17s / 6s : 0,227
+ normal, 20s / 6s : 0,173
+ small, 35s / 20s : 0,162
+ archive, 82s / 26s : 0,158
+```
+
+With 1 million aligned PacBio Revio records, on the same system. Also
+using one thread only:
+
+|Scramble opts. |Size(MB) |Enc(s)|Dec(s)|Codecs used |
+|--------------------|--------:|-----:|-----:|---------------------------|
+|-O bam -1 | 3061| 97.5| 16.0|bgzf(libdeflate) |
+|-O bam (default) | 2891| 128.4| 15.3|bgzf(libdeflate) |
+|-O bam -9 | 2651|2314.7| 16.4|bgzf(libdeflate) |
+||||||
+|-V2.0 -X fast | 1334| 80.3| 23.9|(default, level 1) |
+|-V2.0 (default) | 1206| 111.2| 25.1|(default) |
+|-V2.0 -X small | 1048| 276.3| 98.7|bzip2 |
+|-V2.0 -X archive | 1042| 294.2| 98.5|bzip2 |
+||||||
+|-V3.0 -X fast | 1164| 67.3| 18.5|(default, level 1) |
+|-V3.0 (default) | 1016| 64.5| 26.4|(default) |
+|-V3.0 -X small | 1003| 124.8| 32.2|bzip2 |
+|-V3.0 -X archive | 997| 162.4| 34.7|bzip2 |
+||||||
+|-V3.1 -X fast | 1161| 56.8| 17.6|rANS++ |
+|-V3.1 (default) | 943| 66.0| 18.5|rANS++,tok3 |
+|-V3.1 -X small | 892| 142.7| 81.8|rANS++,tok3,fqz |
+|-V3.1 -X archive | 875| 288.9| 97.6|rANS++,tok3,fqz,bzip2,arith|
+||||||
+|-V4.0 -X fast | 1160| 53.6| 17.6|rANS++ |
+|-V4.0 (default) | 941| 60.9| 17.7|rANS++,tok3 |
+|-V4.0 -X small | 892| 137.6| 78.8|rANS++,tok3,fqz |
+|-V4.0 -X archive | 874| 283.6| 87.9|rANS++,tok3,fqz,bzip2,arith|
+
+```mermaid
+gantt
+ title 1 million PacBio Revio records
+ todayMarker off
+ dateFormat X
+ axisFormat %s
+
+ section BAM
+ -1, 97s / 16s : 0,3061
+ -5, 128s / 15s : 0,2981
+ -9, 2315s / 16s : 0,2651
+ - : 0,0
+
+ section CRAM 2.0
+ fast, 80s / 24s : 0,1334
+ normal, 111s / 25s : 0,1206
+ small, 276s / 32s : 0,1048
+ archive, 294s / 35s : 0,1042
+ - : 0,0
+
+ section CRAM 3.0
+ fast, 67s / 18s : 0,1164
+ normal, 64s / 26s : 0,1016
+ small, 125s / 32s : 0,1003
+ archive, 162s / 35s : 0, 997
+ - : 0,0
+
+ section CRAM 3.1
+ fast, 57s / 18s : 0,1161
+ normal, 66s / 18s : 0, 943
+ small, 143s / 82s : 0, 892
+ archive, 289s / 97s : 0, 875
+ - : 0,0
+
+ section CRAM 4.0
+ fast, 54s / 18s : 0,1160
+ normal, 61s / 18s : 0, 941
+ small, 128s / 79s : 0, 892
+ archive, 284s / 88s : 0, 874
+```
+
Building
========
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
dnl Process this file with autoconf to produce a configure script.
-AC_INIT(io_lib, 1.15.0)
+AC_INIT(io_lib, 1.15.1)
IOLIB_VERSION=$PACKAGE_VERSION
IOLIB_VERSION_MAJOR=`expr "$PACKAGE_VERSION" : '\([[0-9]]*\)'`
IOLIB_VERSION_MINOR=`expr "$PACKAGE_VERSION" : '[[0-9]]*\.\([[0-9]]*\)'`
@@ -69,7 +69,7 @@ AX_SUBDIRS_CONFIGURE([htscodecs],[[--disable-shared],[--with-pic]])
# libstaden-read.so.1.1.0
VERS_CURRENT=15
-VERS_REVISION=3
+VERS_REVISION=4
VERS_AGE=1
AC_SUBST(VERS_CURRENT)
AC_SUBST(VERS_REVISION)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+staden-io-lib (1.15.1-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version 1.15.1
+ * d/control: drop redundant Priority: optional.
+ * d/control: drop redundant Rules-Requires-Root: no.
+ * d/control: declare compliance to standards version 4.7.3.
+ * d/watch: move to uscan v5 Github template.
+ * d/control: remove version on libstaden-read14 conflict.
+ * d/libstaden-read14t64.lintian-overrides: remove.
+ This file held a new ununsed lintian override.
+ * fix_fseeko.patch: normalize Last-Update timestamp.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 22 Feb 2026 18:24:42 +0100
+
staden-io-lib (1.15.0-1.1) unstable; urgency=medium
* Non-maintainer upload.
=====================================
debian/control
=====================================
@@ -5,7 +5,6 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Thorsten Alteholz <debian at alteholz.de>,
Michael R. Crusoe <crusoe at debian.org>
Section: science
-Priority: optional
Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
zlib1g-dev,
libcurl4-gnutls-dev | libcurl4-nss-dev,
@@ -13,11 +12,10 @@ Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13),
d-shlibs (>= 0.106),
libbz2-dev,
liblzma-dev
-Standards-Version: 4.6.2
+Standards-Version: 4.7.3
Vcs-Browser: https://salsa.debian.org/med-team/staden-io-lib
Vcs-Git: https://salsa.debian.org/med-team/staden-io-lib.git
Homepage: https://github.com/jkbonfield/io_lib
-Rules-Requires-Root: no
Package: staden-io-lib-utils
Architecture: any
@@ -53,7 +51,7 @@ Description: development files for libstaden-read
Package: libstaden-read14t64
Provides: ${t64:Provides}
Replaces: libstaden-read14
-Conflicts: libstaden-read14 (<< ${source:Version})
+Conflicts: libstaden-read14
Architecture: any
Multi-Arch: same
Section: libs
=====================================
debian/libstaden-read14t64.lintian-overrides deleted
=====================================
@@ -1 +0,0 @@
-libstaden-read14t64: package-name-doesnt-match-sonames libstaden-read14
=====================================
debian/patches/fix_fseeko.patch
=====================================
@@ -1,6 +1,6 @@
Author: James Bonfield <jkb at sanger.ac.uk>,
James Cowgill <jcowgill at debian.org>
-Last-Update: Thu, 7 Dec 2017 18:09:16 +0000
+Last-Update: 2017-12-07
Bug-Debian: https://bugs.debian.org/876840
Origin: Upstream
Forwarded: not-needed
=====================================
debian/watch
=====================================
@@ -1,4 +1,8 @@
-version=4
+Version: 5
-opts="uversionmangle=s/-/./g,repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/jkbonfield/io_lib/tags .*/io_lib- at ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Owner: jkbonfield
+Project: io_lib
+Dversionmangle: auto
+Repacksuffix: +dfsg
+Uversionmangle: s/-/./g
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/86843f4fac17197302a36aaefae4321311ca4ead...8238f2da0967b1ab9d72d6624a74e7a40d3b369e
--
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/86843f4fac17197302a36aaefae4321311ca4ead...8238f2da0967b1ab9d72d6624a74e7a40d3b369e
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