[med-svn] r17247 - in trunk/packages/staden-io-lib/tags: . 1.13.7-1/debian 1.13.7-1/debian/patches
Charles Plessy
plessy at moszumanska.debian.org
Thu Jun 19 23:15:16 UTC 2014
Author: plessy
Date: 2014-06-19 23:15:16 +0000 (Thu, 19 Jun 2014)
New Revision: 17247
Added:
trunk/packages/staden-io-lib/tags/1.13.7-1/
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series
Removed:
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/fix-bam-read.patch
trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series
Log:
[svn-buildpackage] Tagging staden-io-lib 1.13.7-1
Deleted: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/changelog 2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog 2014-06-19 23:15:16 UTC (rev 17247)
@@ -1,133 +0,0 @@
-staden-io-lib (1.13.5-3) unstable; urgency=medium
-
- * debian/rules: fix permissions in arch=all package only when
- it is really built
- Closes: #745692
-
- -- Andreas Tille <tille at debian.org> Thu, 24 Apr 2014 08:16:30 +0200
-
-staden-io-lib (1.13.5-2) unstable; urgency=medium
-
- * use dh-autoreconf
- Closes: 744664
- * Add autopkgtest using new staden-io-lib-examples package
-
- -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2014 13:08:48 +0200
-
-staden-io-lib (1.13.5-1.1) unstable; urgency=medium
-
- * Non-maintainer upload.
- * Fix io_lib/bam.c read
- Patch by Aleksandar Zlicic
- Add fix-bam-read.patch
- Closes: #736565
-
- -- Anibal Monsalve Salazar <anibal at debian.org> Tue, 01 Apr 2014 04:19:52 +0100
-
-staden-io-lib (1.13.5-1) unstable; urgency=medium
-
- * New upstream release.
- * debian/libstaden-read1.symbols: updated symbols.
- * debian/patches/pathmax.patch: refreshed.
- * debian/patches/fix_bufferoverflow.patch: removed (applied upstream).
-
- -- Charles Plessy <plessy at debian.org> Sat, 15 Mar 2014 12:05:00 +0900
-
-staden-io-lib (1.13.3-2) unstable; urgency=medium
-
- * debian/patches/fix_bufferoverflow.patch: Fix buffer overflow
- Thanks to James Bonfield <jkb at sanger.ac.uk> (upstream) for the patch.
- Closes: #729276
-
- -- Andreas Tille <tille at debian.org> Thu, 12 Dec 2013 13:42:21 +0100
-
-staden-io-lib (1.13.3-1) unstable; urgency=low
-
- * New upstream release. Closes: #715753, #715877, #715878, #715879, #715953.
-
- [ Adam Conrad ]
- * Use dh_autotools-dev to update config.{sub,guess} for new ports.
-
- [ Charles Plessy ]
- * Updated symbols file: some symbols have been removed, but they relate
- to obsolete code that is not expected to be used.
- * Conforms to Policy 3.9.5.
-
- -- Charles Plessy <plessy at debian.org> Sat, 30 Nov 2013 18:11:11 +0900
-
-staden-io-lib (1.13.2-3) unstable; urgency=low
-
- * debian/patches: add patch to build on hurd_i386
- * no need to remove package from mips anymore (Closes: #726875)
-
- -- Thorsten Alteholz <debian at alteholz.de> Mon, 21 Oct 2013 18:10:59 +0200
-
-staden-io-lib (1.13.2-2) unstable; urgency=low
-
- * Restore and update symbols file debian/libstaden-read1.symbols.
-
- -- Charles Plessy <plessy at debian.org> Sat, 10 Aug 2013 12:10:59 +0900
-
-staden-io-lib (1.13.2-1) unstable; urgency=low
-
- [ Charles Plessy ]
- * New upstream release (Closes: #710227).
- * Use Debhelper 9.
- * Removed obsolete DM-Upload-Allowed field.
- * Machine-readable Debian copyright file.
- * Normalised debian/control with config-model-edit.
- * New symbols for libstaden-read1.
- * Search for libraries in tmp/usr/lib/x86_64-linux-gnu/.
- * Removed Breaks and Replaces (staden-io-lib-utils) satisfied in oldstable.
- * Normalised VCS URLs following Lintian's standard.
-
- [ Andreas Tille ]
- * debian/source/format: 3.0 (quilt)
- * debian/control: Build-Depends libcurl4-gnutls-dev
- Closes: #710243
- * debian/libstaden-read1.symbols: Deleted because it simply breaks build.
- * debian/rules: Make use of d-shlibs which should help closing bug
- #710225 because it raises a flag if there is a new ABI
- * provide some help2man created manpages
-
- -- Andreas Tille <tille at debian.org> Wed, 07 Aug 2013 14:31:36 +0200
-
-staden-io-lib (1.12.4-1) unstable; urgency=low
-
- * New upstream release, with changes on endianness detection
- (closes: #579239).
- * Build on all architectures, (debian/control).
- * Added library symbols file (debian/libstaden-read1.symbols).
- * Incremented Standards-Version to reflect conformance with Policy 3.9.1
- (debian/control, no changes needed).
- * Moved io_lib-config from staden-io-lib-utils to libstaden-read-dev
- (debian/rules, debian/control).
-
- -- Charles Plessy <plessy at debian.org> Tue, 27 Jul 2010 21:07:57 +0900
-
-staden-io-lib (1.12.2-2) unstable; urgency=low
-
- * Restrict staden-io-lib to i386 and amd64 platforms, which are the
- only ones where it is known to work and be used (debian/control).
- * Provide a patch for helping people interested in building this
- package on other architectures (debian/endianness.patch).
- * Incremented Standards-Version to reflect conformance with Policy 3.8.4
- (debian/control, no changes needed).
-
- -- Charles Plessy <plessy at debian.org> Sat, 22 May 2010 22:50:35 +0900
-
-staden-io-lib (1.12.2-1) unstable; urgency=low
-
- * New upstream release: extra options in srf2fastq and API changes in
- HashTable code.
- * Removed the libtool ‘.la’ library (debian/staden-read-dev.install).
- * Incremented Standards-Version to reflect conformance with Policy 3.8.3
- (no changes needed).
-
- -- Charles Plessy <plessy at debian.org> Sun, 17 Jan 2010 22:09:42 +0900
-
-staden-io-lib (1.12.1-1) unstable; urgency=low
-
- * Initial release (Closes: #530753)
-
- -- Charles Plessy <plessy at debian.org> Mon, 10 Aug 2009 23:32:59 +0900
Copied: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog (from rev 17246, trunk/packages/staden-io-lib/trunk/debian/changelog)
===================================================================
--- trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog (rev 0)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/changelog 2014-06-19 23:15:16 UTC (rev 17247)
@@ -0,0 +1,142 @@
+staden-io-lib (1.13.7-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Removed debian/patches/fix-bam-read.patch, applied upstream.
+ * debian/libstaden-read1.symbols: updated. Some symbols are missing but
+ it is in area of code that are considered beta (in my understanding).
+
+ -- Charles Plessy <plessy at debian.org> Fri, 20 Jun 2014 08:04:00 +0900
+
+staden-io-lib (1.13.5-3) unstable; urgency=medium
+
+ * debian/rules: fix permissions in arch=all package only when
+ it is really built
+ Closes: #745692
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Apr 2014 08:16:30 +0200
+
+staden-io-lib (1.13.5-2) unstable; urgency=medium
+
+ * use dh-autoreconf
+ Closes: 744664
+ * Add autopkgtest using new staden-io-lib-examples package
+
+ -- Andreas Tille <tille at debian.org> Mon, 14 Apr 2014 13:08:48 +0200
+
+staden-io-lib (1.13.5-1.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Fix io_lib/bam.c read
+ Patch by Aleksandar Zlicic
+ Add fix-bam-read.patch
+ Closes: #736565
+
+ -- Anibal Monsalve Salazar <anibal at debian.org> Tue, 01 Apr 2014 04:19:52 +0100
+
+staden-io-lib (1.13.5-1) unstable; urgency=medium
+
+ * New upstream release.
+ * debian/libstaden-read1.symbols: updated symbols.
+ * debian/patches/pathmax.patch: refreshed.
+ * debian/patches/fix_bufferoverflow.patch: removed (applied upstream).
+
+ -- Charles Plessy <plessy at debian.org> Sat, 15 Mar 2014 12:05:00 +0900
+
+staden-io-lib (1.13.3-2) unstable; urgency=medium
+
+ * debian/patches/fix_bufferoverflow.patch: Fix buffer overflow
+ Thanks to James Bonfield <jkb at sanger.ac.uk> (upstream) for the patch.
+ Closes: #729276
+
+ -- Andreas Tille <tille at debian.org> Thu, 12 Dec 2013 13:42:21 +0100
+
+staden-io-lib (1.13.3-1) unstable; urgency=low
+
+ * New upstream release. Closes: #715753, #715877, #715878, #715879, #715953.
+
+ [ Adam Conrad ]
+ * Use dh_autotools-dev to update config.{sub,guess} for new ports.
+
+ [ Charles Plessy ]
+ * Updated symbols file: some symbols have been removed, but they relate
+ to obsolete code that is not expected to be used.
+ * Conforms to Policy 3.9.5.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 30 Nov 2013 18:11:11 +0900
+
+staden-io-lib (1.13.2-3) unstable; urgency=low
+
+ * debian/patches: add patch to build on hurd_i386
+ * no need to remove package from mips anymore (Closes: #726875)
+
+ -- Thorsten Alteholz <debian at alteholz.de> Mon, 21 Oct 2013 18:10:59 +0200
+
+staden-io-lib (1.13.2-2) unstable; urgency=low
+
+ * Restore and update symbols file debian/libstaden-read1.symbols.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 10 Aug 2013 12:10:59 +0900
+
+staden-io-lib (1.13.2-1) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * New upstream release (Closes: #710227).
+ * Use Debhelper 9.
+ * Removed obsolete DM-Upload-Allowed field.
+ * Machine-readable Debian copyright file.
+ * Normalised debian/control with config-model-edit.
+ * New symbols for libstaden-read1.
+ * Search for libraries in tmp/usr/lib/x86_64-linux-gnu/.
+ * Removed Breaks and Replaces (staden-io-lib-utils) satisfied in oldstable.
+ * Normalised VCS URLs following Lintian's standard.
+
+ [ Andreas Tille ]
+ * debian/source/format: 3.0 (quilt)
+ * debian/control: Build-Depends libcurl4-gnutls-dev
+ Closes: #710243
+ * debian/libstaden-read1.symbols: Deleted because it simply breaks build.
+ * debian/rules: Make use of d-shlibs which should help closing bug
+ #710225 because it raises a flag if there is a new ABI
+ * provide some help2man created manpages
+
+ -- Andreas Tille <tille at debian.org> Wed, 07 Aug 2013 14:31:36 +0200
+
+staden-io-lib (1.12.4-1) unstable; urgency=low
+
+ * New upstream release, with changes on endianness detection
+ (closes: #579239).
+ * Build on all architectures, (debian/control).
+ * Added library symbols file (debian/libstaden-read1.symbols).
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.1
+ (debian/control, no changes needed).
+ * Moved io_lib-config from staden-io-lib-utils to libstaden-read-dev
+ (debian/rules, debian/control).
+
+ -- Charles Plessy <plessy at debian.org> Tue, 27 Jul 2010 21:07:57 +0900
+
+staden-io-lib (1.12.2-2) unstable; urgency=low
+
+ * Restrict staden-io-lib to i386 and amd64 platforms, which are the
+ only ones where it is known to work and be used (debian/control).
+ * Provide a patch for helping people interested in building this
+ package on other architectures (debian/endianness.patch).
+ * Incremented Standards-Version to reflect conformance with Policy 3.8.4
+ (debian/control, no changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Sat, 22 May 2010 22:50:35 +0900
+
+staden-io-lib (1.12.2-1) unstable; urgency=low
+
+ * New upstream release: extra options in srf2fastq and API changes in
+ HashTable code.
+ * Removed the libtool ‘.la’ library (debian/staden-read-dev.install).
+ * Incremented Standards-Version to reflect conformance with Policy 3.8.3
+ (no changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Sun, 17 Jan 2010 22:09:42 +0900
+
+staden-io-lib (1.12.1-1) unstable; urgency=low
+
+ * Initial release (Closes: #530753)
+
+ -- Charles Plessy <plessy at debian.org> Mon, 10 Aug 2009 23:32:59 +0900
Deleted: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/copyright 2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright 2014-06-19 23:15:16 UTC (rev 17247)
@@ -1,169 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Source: http://qa.debian.org/watch/sf.php/staden/io_lib-1.13.5.tar.gz
-
-Files: *
-Copyright: © 1994 Medical Research Council
- © Genome Research Ltd (GRL)
-License: GRL or MRC
-Upstream-Comment: Newer files and changes are copyright Genome Research Ltd
- using the following compatible BSD licence. Disentangling which is which is
- somewhat tricky, but it's sufficient to say that work in the CVS/SVN tree from
- August 2002 will be bound by the GRL licence instead.
-
-Files: io_lib/arith_static.c
-Copyright: © 2003 Eugene Shelwien
- © 2014 Genome Research Ltd.
-License: GRL-new
-Comment: Range Coder portion derived from code by Eugene Shelwien (c) 2003.
-
-Files: io_lib/binning.h
-Copyright: © 2014 Genome Research Ltd.
-License: GRL-new
-
-Files: io_lib/rANS_static.c
-Copyright: public domain parts by Fabian 'ryg' Giesen
- © 2014 Genome Research Ltd.
-License: GRL-new
-
-Files: io_lib/open_trace_file.c
-Copyright: © 2001-2005 454 Life Sciences Corporation
-License: GRL or MRC, and 454
- This file contains some source code owned by 454 Life Sciences Corporation.
-
-Files: io_lib/sff.c:
-Copyright: © Genome Research Limited (GRL)
- © 2001-2005 454 Life Sciences Corporation.
-License: GRL and 454
- This file contains some extracts from a file owened by the 454 Life Sciences Corporation.
-
-Files: io_lib/md5.*
-Copyright: see License
-License: says-public-domain
- This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
- MD5 Message-Digest Algorithm (RFC 1321).
- .
- Homepage:
- http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
- .
- Author:
- Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
- .
- This software was written by Alexander Peslyak in 2001. No copyright is
- claimed, and the software is hereby placed in the public domain.
- In case this attempt to disclaim copyright and place the software in the
- public domain is deemed null and void, then the software is
- Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
- general public under the following terms:
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted.
- .
- There's ABSOLUTELY NO WARRANTY, express or implied.
- .
- (This is a heavily cut-down "BSD license".)
- .
- This differs from Colin Plumb's older public domain implementation in that
- no exactly 32-bit integer data type is required (any 32-bit or wider
- unsigned integer data type will do), there's no compile-time endianness
- configuration, and the function prototypes match OpenSSL's. No code from
- Colin Plumb's implementation has been reused; this comment merely compares
- the properties of the two independent implementations.
- .
- The primary goals of this implementation are portability and ease of use.
- It is meant to be fast, but not as fast as possible. Some known
- optimizations are not included to reduce source code size and avoid
- compile-time configuration.
-
-Files: debian/*
-Copyright: 2008–2009 Charles Plessy <plessy at debian.org>
-License: PD
- Please treat these files as if they were in your country’s public domain.
-
-License: 454
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
- .
- IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
- .
- Permission to use, copy, modify and distribute this software and its
- documentation for any purpose is hereby granted without fee, provided
- that this copyright and notice appears in all copies.
-
-License: GRL
- Copyright (c), Genome Research Ltd (GRL).
- All rights reserved.
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- .
- * Redistributions of source code must retain the above copyright
- notice, this list of conditions and the following disclaimer.
- .
- * Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials
- provided with the distribution.
- .
- * Neither the name of the Genome Research Limited nor the
- names of its contributors may be used to endorse or promote
- products derived from this software without specific prior
- written permission.
- .
- THIS SOFTWARE IS PROVIDED BY GRL ``AS IS'' AND ANY EXPRESS OR
- IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL GRL BE LIABLE FOR ANY DIRECT,
- INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
- STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
- OF THE POSSIBILITY OF SUCH DAMAGE.
-
-License: GRL-new
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
- .
- 1. Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
- .
- 2. Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the following
- disclaimer in the documentation and/or other materials provided
- with the distribution.
- .
- 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
- Institute nor the names of its contributors may be used to endorse
- or promote products derived from this software without specific
- prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
- IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
- TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
- PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
- LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
- SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
- LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-License: MRC
- Copyright (c) Medical Research Council 1994. All rights reserved.
- .
- Permission to use, copy, modify and distribute this software and its
- documentation for any purpose is hereby granted without fee, provided that
- this copyright and notice appears in all copies.
- .
- This file was written by James Bonfield, Simon Dear, Rodger Staden,
- as part of the Staden Package at the MRC Laboratory of Molecular
- Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
- .
- MRC disclaims all warranties with regard to this software.
-
Copied: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright (from rev 17246, trunk/packages/staden-io-lib/trunk/debian/copyright)
===================================================================
--- trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright (rev 0)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/copyright 2014-06-19 23:15:16 UTC (rev 17247)
@@ -0,0 +1,169 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://qa.debian.org/watch/sf.php/staden/io_lib-1.13.7.tar.gz
+
+Files: *
+Copyright: © 1994 Medical Research Council
+ © Genome Research Ltd (GRL)
+License: GRL or MRC
+Upstream-Comment: Newer files and changes are copyright Genome Research Ltd
+ using the following compatible BSD licence. Disentangling which is which is
+ somewhat tricky, but it's sufficient to say that work in the CVS/SVN tree from
+ August 2002 will be bound by the GRL licence instead.
+
+Files: io_lib/arith_static.c
+Copyright: © 2003 Eugene Shelwien
+ © 2014 Genome Research Ltd.
+License: GRL-new
+Comment: Range Coder portion derived from code by Eugene Shelwien (c) 2003.
+
+Files: io_lib/binning.h
+Copyright: © 2014 Genome Research Ltd.
+License: GRL-new
+
+Files: io_lib/rANS_static.c
+Copyright: public domain parts by Fabian 'ryg' Giesen
+ © 2014 Genome Research Ltd.
+License: GRL-new
+
+Files: io_lib/open_trace_file.c
+Copyright: © 2001-2005 454 Life Sciences Corporation
+License: GRL or MRC, and 454
+ This file contains some source code owned by 454 Life Sciences Corporation.
+
+Files: io_lib/sff.c:
+Copyright: © Genome Research Limited (GRL)
+ © 2001-2005 454 Life Sciences Corporation.
+License: GRL and 454
+ This file contains some extracts from a file owened by the 454 Life Sciences Corporation.
+
+Files: io_lib/md5.*
+Copyright: see License
+License: says-public-domain
+ This is an OpenSSL-compatible implementation of the RSA Data Security, Inc.
+ MD5 Message-Digest Algorithm (RFC 1321).
+ .
+ Homepage:
+ http://openwall.info/wiki/people/solar/software/public-domain-source-code/md5
+ .
+ Author:
+ Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
+ .
+ This software was written by Alexander Peslyak in 2001. No copyright is
+ claimed, and the software is hereby placed in the public domain.
+ In case this attempt to disclaim copyright and place the software in the
+ public domain is deemed null and void, then the software is
+ Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
+ general public under the following terms:
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted.
+ .
+ There's ABSOLUTELY NO WARRANTY, express or implied.
+ .
+ (This is a heavily cut-down "BSD license".)
+ .
+ This differs from Colin Plumb's older public domain implementation in that
+ no exactly 32-bit integer data type is required (any 32-bit or wider
+ unsigned integer data type will do), there's no compile-time endianness
+ configuration, and the function prototypes match OpenSSL's. No code from
+ Colin Plumb's implementation has been reused; this comment merely compares
+ the properties of the two independent implementations.
+ .
+ The primary goals of this implementation are portability and ease of use.
+ It is meant to be fast, but not as fast as possible. Some known
+ optimizations are not included to reduce source code size and avoid
+ compile-time configuration.
+
+Files: debian/*
+Copyright: 2008–2009 Charles Plessy <plessy at debian.org>
+License: PD
+ Please treat these files as if they were in your country’s public domain.
+
+License: 454
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ .
+ IN NO EVENT SHALL LICENSOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE.
+ .
+ Permission to use, copy, modify and distribute this software and its
+ documentation for any purpose is hereby granted without fee, provided
+ that this copyright and notice appears in all copies.
+
+License: GRL
+ Copyright (c), Genome Research Ltd (GRL).
+ All rights reserved.
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials
+ provided with the distribution.
+ .
+ * Neither the name of the Genome Research Limited nor the
+ names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior
+ written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY GRL ``AS IS'' AND ANY EXPRESS OR
+ IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL GRL BE LIABLE FOR ANY DIRECT,
+ INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+ STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
+ OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: GRL-new
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ 1. Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ .
+ 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ Institute nor the names of its contributors may be used to endorse
+ or promote products derived from this software without specific
+ prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License: MRC
+ Copyright (c) Medical Research Council 1994. All rights reserved.
+ .
+ Permission to use, copy, modify and distribute this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ this copyright and notice appears in all copies.
+ .
+ This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ as part of the Staden Package at the MRC Laboratory of Molecular
+ Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ .
+ MRC disclaims all warranties with regard to this software.
+
Deleted: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/libstaden-read1.symbols 2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols 2014-06-19 23:15:16 UTC (rev 17247)
@@ -1,654 +0,0 @@
-libstaden-read.so.1 libstaden-read1 #MINVER#
- ArrayCreate at Base 1.12.4
- ArrayDestroy at Base 1.12.4
- ArrayError at Base 1.12.4
- ArrayErrorString at Base 1.12.4
- ArrayExtend at Base 1.12.4
- ArrayRef at Base 1.12.4
- HashFileCreate at Base 1.12.4
- HashFileDestroy at Base 1.12.4
- HashFileExtract at Base 1.12.4
- HashFileFopen at Base 1.12.4
- HashFileLoad at Base 1.12.4
- HashFileOpen at Base 1.12.4
- HashFileQuery at Base 1.12.4
- HashFileSave at Base 1.12.4
- HashHsieh at Base 1.12.4
- HashJenkins3 at Base 1.12.4
- HashJenkins at Base 1.12.4
- HashTableAdd at Base 1.12.4
- HashTableCreate at Base 1.12.4
- HashTableDel at Base 1.12.4
- HashTableDestroy at Base 1.12.4
- HashTableDump at Base 1.12.4
- HashTableIterCreate at Base 1.12.4
- HashTableIterDestroy at Base 1.12.4
- HashTableIterNext at Base 1.12.4
- HashTableIterReset at Base 1.12.4
- HashTableNext at Base 1.12.4
- HashTableRemove at Base 1.12.4
- HashTableResize at Base 1.12.4
- HashTableSearch at Base 1.12.4
- HashTableStats at Base 1.12.4
- HashTcl at Base 1.12.4
- MD5_Final at Base 1.13.1
- MD5_Init at Base 1.13.1
- MD5_Update at Base 1.13.1
- abi_reset_data_counts at Base 1.12.4
- abi_set_data_counts at Base 1.12.4
- arith_compress at Base 1.13.5
- arith_compress_O0 at Base 1.13.5
- arith_compress_O1 at Base 1.13.5
- arith_uncompress at Base 1.13.5
- arith_uncompress_O0 at Base 1.13.5
- arith_uncompress_O1 at Base 1.13.5
- bam_add_raw at Base 1.13.2
- bam_aux_A at Base 1.13.1
- bam_aux_Z at Base 1.13.1
- bam_aux_add at Base 1.13.1
- bam_aux_add_data at Base 1.13.1
- bam_aux_add_from_sam at Base 1.13.1
- bam_aux_add_vec at Base 1.13.1
- bam_aux_d at Base 1.13.1
- bam_aux_f at Base 1.13.1
- bam_aux_find at Base 1.13.1
- bam_aux_i at Base 1.13.1
- bam_aux_iter at Base 1.13.1
- bam_aux_size_vec at Base 1.13.1
- bam_close at Base 1.13.1
- bam_construct_seq at Base 1.13.1
- bam_copy at Base 1.13.2
- bam_dup at Base 1.13.2
- bam_get_seq at Base 1.13.1
- bam_next_seq at Base 1.13.1
- bam_open at Base 1.13.1
- bam_put_seq at Base 1.13.1
- bam_set_option at Base 1.13.2
- bam_set_voption at Base 1.13.2
- bam_write_header at Base 1.13.1
- be_read_int_1 at Base 1.12.4
- be_read_int_2 at Base 1.12.4
- be_read_int_4 at Base 1.12.4
- be_read_int_8 at Base 1.12.4
- be_write_int_1 at Base 1.12.4
- be_write_int_2 at Base 1.12.4
- be_write_int_4 at Base 1.12.4
- be_write_int_8 at Base 1.12.4
- bgzf_decode_thread at Base 1.13.2
- bgzf_encode_thread at Base 1.13.2
- bit_reverse at Base 1.12.4
- block_create at Base 1.12.4
- block_destroy at Base 1.12.4
- block_resize at Base 1.12.4
- c2fstr at Base 1.12.4
- calc_bit_lengths at Base 1.12.4
- close_fofn at Base 1.12.4
- codes2codeset at Base 1.12.4
- compress_chunk at Base 1.12.4
- compress_file at Base 1.12.4
- compress_int2str at Base 1.12.4
- compress_str2int at Base 1.12.4
- compress_ztr at Base 1.12.4
- compressed_file_exists at Base 1.12.4
- conf2str at Base 1.12.4
- construct_trace_name at Base 1.12.4
- cram_beta_decode_char at Base 1.13.2
- cram_beta_decode_free at Base 1.13.1
- cram_beta_decode_init at Base 1.13.1
- cram_beta_decode_int at Base 1.13.2
- cram_beta_encode_char at Base 1.13.1
- cram_beta_encode_free at Base 1.13.1
- cram_beta_encode_init at Base 1.13.1
- cram_beta_encode_int at Base 1.13.1
- cram_beta_encode_store at Base 1.13.1
- cram_block_method2str at Base 1.13.1
- cram_byte_array_len_decode at Base 1.13.1
- cram_byte_array_len_decode_free at Base 1.13.1
- cram_byte_array_len_decode_init at Base 1.13.1
- cram_byte_array_len_encode at Base 1.13.1
- cram_byte_array_len_encode_free at Base 1.13.1
- cram_byte_array_len_encode_init at Base 1.13.1
- cram_byte_array_len_encode_store at Base 1.13.1
- cram_byte_array_stop_decode_block at Base 1.13.1
- cram_byte_array_stop_decode_char at Base 1.13.1
- cram_byte_array_stop_decode_free at Base 1.13.1
- cram_byte_array_stop_decode_init at Base 1.13.1
- cram_byte_array_stop_encode at Base 1.13.1
- cram_byte_array_stop_encode_free at Base 1.13.1
- cram_byte_array_stop_encode_init at Base 1.13.1
- cram_byte_array_stop_encode_store at Base 1.13.1
- cram_close at Base 1.13.1
- cram_compress_block at Base 1.13.1
- cram_content_type2str at Base 1.13.1
- cram_decode_TD at Base 1.13.1
- cram_decode_compression_header at Base 1.13.1
- cram_decode_slice at Base 1.13.1
- cram_decode_slice_header at Base 1.13.1
- cram_decode_slice_mt at Base 1.13.2
- cram_decode_slice_thread at Base 1.13.2
- cram_decoder_init at Base 1.13.1
- cram_encode_compression_header at Base 1.13.1
- cram_encode_container at Base 1.13.1
- cram_encode_slice_header at Base 1.13.1
- cram_encoder_init at Base 1.13.1
- cram_encoding2str at Base 1.13.1
- cram_eof at Base 1.13.1
- cram_external_decode_block at Base 1.13.1
- cram_external_decode_char at Base 1.13.1
- cram_external_decode_free at Base 1.13.1
- cram_external_decode_init at Base 1.13.1
- cram_external_decode_int at Base 1.13.1
- cram_external_encode at Base 1.13.1
- cram_external_encode_free at Base 1.13.1
- cram_external_encode_init at Base 1.13.1
- cram_external_encode_store at Base 1.13.1
- cram_flush at Base 1.13.1
- cram_flush_container at Base 1.13.1
- cram_flush_container_mt at Base 1.13.2
- cram_flush_thread at Base 1.13.2
- cram_free_block at Base 1.13.1
- cram_free_compression_header at Base 1.13.1
- cram_free_container at Base 1.13.1
- cram_free_file_def at Base 1.13.1
- cram_free_slice at Base 1.13.1
- cram_free_slice_header at Base 1.13.1
- cram_gamma_decode at Base 1.13.1
- cram_gamma_decode_free at Base 1.13.1
- cram_gamma_decode_init at Base 1.13.1
- cram_get_bam_seq at Base 1.13.1
- cram_get_ref at Base 1.13.1
- cram_get_seq at Base 1.13.1
- cram_huffman_decode_char0 at Base 1.13.1
- cram_huffman_decode_char at Base 1.13.1
- cram_huffman_decode_free at Base 1.13.1
- cram_huffman_decode_init at Base 1.13.1
- cram_huffman_decode_int0 at Base 1.13.1
- cram_huffman_decode_int at Base 1.13.1
- cram_huffman_encode_char0 at Base 1.13.1
- cram_huffman_encode_char at Base 1.13.1
- cram_huffman_encode_free at Base 1.13.1
- cram_huffman_encode_init at Base 1.13.1
- cram_huffman_encode_int0 at Base 1.13.1
- cram_huffman_encode_int at Base 1.13.1
- cram_huffman_encode_store at Base 1.13.1
- cram_index_free at Base 1.13.1
- cram_index_load at Base 1.13.1
- cram_index_query at Base 1.13.1
- cram_load_reference at Base 1.13.1
- cram_new_block at Base 1.13.1
- cram_new_compression_header at Base 1.13.1
- cram_new_container at Base 1.13.1
- cram_new_metrics at Base 1.13.1
- cram_new_slice at Base 1.13.1
- cram_open at Base 1.13.1
- cram_put_bam_seq at Base 1.13.1
- cram_read_SAM_hdr at Base 1.13.1
- cram_read_block at Base 1.13.1
- cram_read_container at Base 1.13.1
- cram_read_file_def at Base 1.13.1
- cram_read_slice at Base 1.13.1
- cram_ref_decr at Base 1.13.2
- cram_ref_incr at Base 1.13.2
- cram_ref_load at Base 1.13.2
- cram_seek at Base 1.13.1
- cram_seek_to_refpos at Base 1.13.1
- cram_set_option at Base 1.13.1
- cram_set_voption at Base 1.13.1
- cram_stats_add at Base 1.13.1
- cram_stats_create at Base 1.13.1
- cram_stats_del at Base 1.13.1
- cram_stats_dump at Base 1.13.1
- cram_stats_encoding at Base 1.13.1
- cram_stats_free at Base 1.13.1
- cram_subexp_decode at Base 1.13.1
- cram_subexp_decode_free at Base 1.13.1
- cram_subexp_decode_init at Base 1.13.1
- cram_uncompress_block at Base 1.13.1
- cram_write_SAM_hdr at Base 1.13.1
- cram_write_block at Base 1.13.1
- cram_write_container at Base 1.13.1
- cram_write_file_def at Base 1.13.1
-#MISSING: 1.13.3-1# ctfFRead at Base 1.12.4
-#MISSING: 1.13.3-1# ctfFWrite at Base 1.12.4
- decode_sff_common_header at Base 1.12.4
- decode_sff_read_header at Base 1.12.4
- decorrelate1 at Base 1.12.4
- decorrelate1dyn at Base 1.12.4
- decorrelate2 at Base 1.12.4
- decorrelate2dyn at Base 1.12.4
- decorrelate4 at Base 1.12.4
- delete_ztr at Base 1.12.4
- determine_trace_type at Base 1.12.4
- dstring_append at Base 1.13.1
- dstring_append_char at Base 1.13.1
- dstring_append_hex_encoded at Base 1.13.1
- dstring_append_int at Base 1.13.1
- dstring_appendf at Base 1.13.1
- dstring_create at Base 1.13.1
- dstring_create_with at Base 1.13.1
- dstring_delete at Base 1.13.1
- dstring_destroy at Base 1.13.1
- dstring_dinsert at Base 1.13.1
- dstring_dreplace at Base 1.13.1
- dstring_empty at Base 1.13.1
- dstring_escape_html at Base 1.13.1
- dstring_find at Base 1.13.1
- dstring_find_replace at Base 1.13.1
- dstring_find_replace_all at Base 1.13.1
- dstring_htmlise_links at Base 1.13.1
- dstring_insert at Base 1.13.1
- dstring_insertf at Base 1.13.1
- dstring_length at Base 1.13.1
- dstring_nappend at Base 1.13.1
- dstring_ninsert at Base 1.13.1
- dstring_nprepend at Base 1.13.1
- dstring_perror at Base 1.13.1
- dstring_prepend at Base 1.13.1
- dstring_prependf at Base 1.13.1
- dstring_refresh_length at Base 1.13.1
- dstring_replace at Base 1.13.1
- dstring_resize at Base 1.13.1
- dstring_str at Base 1.13.1
- dstring_to_html at Base 1.13.1
- dstring_vinsertf at Base 1.13.1
- dump_labels at Base 1.12.4
- eflt_feature_ids at Base 1.12.4
- encode_sff_common_header at Base 1.12.4
- encode_sff_read_header at Base 1.12.4
- errout at Base 1.12.4
- exp2read at Base 1.12.4
- exp_close at Base 1.12.4
- exp_create_info at Base 1.12.4
- exp_create_range at Base 1.12.4
- exp_destroy_info at Base 1.12.4
- exp_extract_range at Base 1.12.4
- exp_fread_info at Base 1.12.4
- exp_get_feature_index at Base 1.12.4
- exp_get_int at Base 1.12.4
- exp_get_rng at Base 1.12.4
- exp_get_str at Base 1.12.4
- exp_mfread_info at Base 1.12.4
- exp_print_file at Base 1.12.4
- exp_print_line at Base 1.12.4
- exp_print_mfile at Base 1.12.4
- exp_print_mline at Base 1.12.4
- exp_print_seq at Base 1.12.4
- exp_put_int at Base 1.12.4
- exp_put_rng at Base 1.12.4
- exp_put_str at Base 1.12.4
- exp_read_info at Base 1.12.4
- exp_set_entry at Base 1.12.4
- expand_8to16 at Base 1.12.4
- expand_8to32 at Base 1.12.4
- expand_cache_path at Base 1.13.1
- expcr_ at Base 1.12.4
- exper_ at Base 1.12.4
- expkil_ at Base 1.12.4
- expopn_ at Base 1.12.4
- expri_ at Base 1.12.4
- exprr_ at Base 1.12.4
- exprs_ at Base 1.12.4
- exprsa_ at Base 1.12.4
- expwi_ at Base 1.12.4
- expwr_ at Base 1.12.4
- expws_ at Base 1.12.4
- expwsa_ at Base 1.12.4
- f2cstr at Base 1.12.4
- fcompress_file at Base 1.12.4
- fdetermine_trace_type at Base 1.12.4
- file_exists at Base 1.12.4
- file_size at Base 1.12.4
- find_file_url at Base 1.13.1
- flen at Base 1.12.4
- follow1 at Base 1.12.4
- fopen_compressed at Base 1.12.4
- fread_abi at Base 1.12.4
- fread_alf at Base 1.12.4
-#MISSING: 1.13.3-1# fread_ctf at Base 1.12.4
- fread_pln at Base 1.12.4
- fread_reading at Base 1.12.4
- fread_scf at Base 1.12.4
- fread_ztr at Base 1.12.4
- free_sff_common_header at Base 1.12.4
- free_sff_read_data at Base 1.12.4
- free_sff_read_header at Base 1.12.4
- freopen_compressed at Base 1.12.4
- fstrlen at Base 1.12.4
- fwrite_abi at Base 1.12.4
- fwrite_alf at Base 1.12.4
-#MISSING: 1.13.3-1# fwrite_ctf at Base 1.12.4
- fwrite_pln at Base 1.12.4
- fwrite_reading at Base 1.12.4
- fwrite_scf at Base 1.12.4
- fwrite_ztr at Base 1.12.4
- generate_code_set at Base 1.12.4
- getABIIndexEntryLW at Base 1.12.4
- getABIIndexEntrySW at Base 1.12.4
- getABIIndexOffset at Base 1.12.4
- getABIString at Base 1.12.4
- getABIint1 at Base 1.12.4
- getABIint2 at Base 1.12.4
- getABIint4 at Base 1.12.4
- get_compression_method at Base 1.12.4
- get_read_conf at Base 1.12.4
- hash64 at Base 1.12.4
- hash at Base 1.12.4
- huffman_codes_destroy at Base 1.12.4
- huffman_codeset_destroy at Base 1.12.4
- huffman_decode at Base 1.12.4
- huffman_multi_decode at Base 1.12.4
- huffman_multi_encode at Base 1.12.4
- ichebcomp at Base 1.12.4
- ichebuncomp at Base 1.12.4
- init_decode_tables at Base 1.12.4
- int32_decode at Base 1.13.1
- int32_encode at Base 1.13.1
- int32_get at Base 1.13.1
- int32_put at Base 1.13.1
- int_to_float at Base 1.12.4
- iolib_get_exp_path at Base 1.12.4
- iolib_get_trace_path at Base 1.12.4
- iolib_set_exp_path at Base 1.12.4
- iolib_set_trace_path at Base 1.12.4
- is_directory at Base 1.12.4
- is_file at Base 1.12.4
- is_scf at Base 1.12.4
- itf8_decode at Base 1.13.1
- itf8_encode at Base 1.13.1
- itf8_put_blk at Base 1.13.1
- le_read_int_1 at Base 1.12.4
- le_read_int_2 at Base 1.12.4
- le_read_int_4 at Base 1.12.4
- le_read_int_8 at Base 1.12.4
- le_write_int_1 at Base 1.12.4
- le_write_int_2 at Base 1.12.4
- le_write_int_4 at Base 1.12.4
- le_write_int_8 at Base 1.12.4
- log2_data at Base 1.12.4
- ltf8_decode at Base 1.13.1
- ltf8_get at Base 1.13.1
- ltf8_put at Base 1.13.1
- memgunzip at Base 1.12.4
- memgzip at Base 1.12.4
- mfascii at Base 1.12.4
- mfclose at Base 1.12.4
- mfcreate at Base 1.12.4
- mfcreate_from at Base 1.12.4
- mfdestroy at Base 1.12.4
- mfdetach at Base 1.12.4
- mfeof at Base 1.12.4
- mfflush at Base 1.12.4
- mfgetc at Base 1.12.4
- mfgets at Base 1.12.4
- mfopen at Base 1.12.4
- mfprintf at Base 1.12.4
- mfread at Base 1.12.4
- mfread_abi at Base 1.12.4
- mfread_alf at Base 1.12.4
-#MISSING: 1.13.3-1# mfread_ctf at Base 1.12.4
- mfread_pln at Base 1.12.4
- mfread_reading at Base 1.12.4
- mfread_scf at Base 1.12.4
- mfread_sff at Base 1.12.4
- mfread_ztr at Base 1.12.4
- mfrecreate at Base 1.12.4
- mfreopen at Base 1.12.4
- mfseek at Base 1.12.4
- mfsteal at Base 1.13.5
- mftell at Base 1.12.4
- mftruncate at Base 1.12.4
- mfwrite at Base 1.12.4
- mfwrite_abi at Base 1.12.4
- mfwrite_alf at Base 1.12.4
-#MISSING: 1.13.3-1# mfwrite_ctf at Base 1.12.4
- mfwrite_pln at Base 1.12.4
- mfwrite_reading at Base 1.12.4
- mfwrite_scf at Base 1.12.4
- mfwrite_ztr at Base 1.12.4
- mkdir_prefix at Base 1.13.1
- mrewind at Base 1.12.4
- mstderr at Base 1.12.4
- mstdin at Base 1.12.4
- mstdout at Base 1.12.4
- mungetc at Base 1.12.4
- myfind at Base 1.12.4
- mystrtok at Base 1.12.4
- new_ztr at Base 1.12.4
- next_symbol at Base 1.12.4
- open_exp_file at Base 1.12.4
- open_exp_mfile at Base 1.12.4
- open_fofn at Base 1.12.4
- open_path_file at Base 1.12.4
- open_path_mfile at Base 1.12.4
- open_trace_file at Base 1.12.4
- open_trace_mfile at Base 1.12.4
- opos2str at Base 1.12.4
- pack_trace_suffix at Base 1.12.4
- paranoid_fclose at Base 1.13.1
- partial_decode_ztr at Base 1.12.4
- pool_alloc at Base 1.12.4
- pool_create at Base 1.12.4
- pool_destroy at Base 1.12.4
- pool_free at Base 1.12.4
- qshift at Base 1.12.4
- rans_compress at Base 1.13.5
- rans_compress_O0 at Base 1.13.5
- rans_compress_O1 at Base 1.13.5
- rans_uncompress at Base 1.13.5
- rans_uncompress_O0 at Base 1.13.5
- rans_uncompress_O1 at Base 1.13.5
- read2exp at Base 1.12.4
- read2scf at Base 1.12.4
- read2ztr at Base 1.12.4
- read_abi at Base 1.12.4
- read_alf at Base 1.12.4
- read_allocate at Base 1.12.4
-#MISSING: 1.13.3-1# read_ctf at Base 1.12.4
- read_deallocate at Base 1.12.4
- read_dup at Base 1.12.4
- read_experiment_redirect at Base 1.12.4
- read_fofn at Base 1.12.4
- read_pln at Base 1.12.4
- read_reading at Base 1.12.4
- read_scf at Base 1.12.4
- read_scf_base at Base 1.12.4
- read_scf_bases3 at Base 1.12.4
- read_scf_bases at Base 1.12.4
- read_scf_comment at Base 1.12.4
- read_scf_header at Base 1.12.4
- read_scf_sample1 at Base 1.12.4
- read_scf_sample2 at Base 1.12.4
- read_scf_samples1 at Base 1.12.4
- read_scf_samples2 at Base 1.12.4
- read_scf_samples31 at Base 1.12.4
- read_scf_samples32 at Base 1.12.4
- read_sections at Base 1.12.4
- read_sff_common_header at Base 1.12.4
- read_sff_read_data at Base 1.12.4
- read_sff_read_header at Base 1.12.4
- read_update_base_positions at Base 1.12.4
- read_update_confidence_values at Base 1.12.4
- recorrelate1 at Base 1.12.4
- recorrelate2 at Base 1.12.4
- recorrelate4 at Base 1.12.4
- refs2id at Base 1.13.1
- refs_free at Base 1.13.2
- remove_extension at Base 1.12.4
- remove_file at Base 1.12.4
- restore_codes at Base 1.12.4
- restore_codes_single at Base 1.12.4
- rle at Base 1.12.4
- sam_hdr_PG_ID at Base 1.13.1
- sam_hdr_add at Base 1.13.1
- sam_hdr_add_PG at Base 1.13.1
- sam_hdr_add_lines at Base 1.13.1
- sam_hdr_decr_ref at Base 1.13.2
- sam_hdr_dump at Base 1.13.1
- sam_hdr_dup at Base 1.13.1
- sam_hdr_find at Base 1.13.1
- sam_hdr_find_key at Base 1.13.1
- sam_hdr_find_line at Base 1.13.1
- sam_hdr_find_rg at Base 1.13.1
- sam_hdr_free at Base 1.13.1
- sam_hdr_incr_ref at Base 1.13.2
- sam_hdr_length at Base 1.13.1
- sam_hdr_link_pg at Base 1.13.1
- sam_hdr_name2ref at Base 1.13.1
- sam_hdr_new at Base 1.13.1
- sam_hdr_parse at Base 1.13.1
- sam_hdr_rebuild at Base 1.13.1
- sam_hdr_str at Base 1.13.1
- sam_hdr_update at Base 1.13.1
- sam_hdr_vadd at Base 1.13.1
- scf2read at Base 1.12.4
- scf_allocate at Base 1.12.4
- scf_deallocate at Base 1.12.4
- scf_delta_samples1 at Base 1.12.4
- scf_delta_samples2 at Base 1.12.4
- scf_version_float2str at Base 1.12.4
- scf_version_str2float at Base 1.12.4
- scram_close at Base 1.13.1
- scram_get_header at Base 1.13.1
- scram_get_refs at Base 1.13.1
- scram_get_seq at Base 1.13.1
- scram_input_bam_block at Base 1.13.2
- scram_line at Base 1.13.2
- scram_next_seq at Base 1.13.1
- scram_open at Base 1.13.1
- scram_put_seq at Base 1.13.1
- scram_set_header at Base 1.13.1
- scram_set_option at Base 1.13.1
- scram_set_refs at Base 1.13.1
- scram_write_header at Base 1.13.1
- set_compression_method at Base 1.12.4
- set_scf_version at Base 1.12.4
- shrink_16to8 at Base 1.12.4
- shrink_32to8 at Base 1.12.4
- srf_construct_cont_hdr at Base 1.12.4
- srf_construct_trace_body at Base 1.12.4
- srf_construct_trace_hdr at Base 1.12.4
- srf_create at Base 1.12.4
- srf_destroy at Base 1.12.4
- srf_destroy_cont_hdr at Base 1.12.4
- srf_destroy_trace_body at Base 1.12.4
- srf_destroy_trace_hdr at Base 1.12.4
- srf_find_trace at Base 1.12.4
- srf_index_add_cont_hdr at Base 1.12.4
- srf_index_add_trace_body at Base 1.12.4
- srf_index_add_trace_hdr at Base 1.12.4
- srf_index_create at Base 1.12.4
- srf_index_destroy at Base 1.12.4
- srf_index_stats at Base 1.12.4
- srf_index_write at Base 1.12.4
- srf_next_block_details at Base 1.12.4
- srf_next_block_type at Base 1.12.4
- srf_next_trace at Base 1.12.4
- srf_next_ztr at Base 1.12.4
- srf_next_ztr_flags at Base 1.12.4
- srf_open at Base 1.12.4
- srf_read_cont_hdr at Base 1.12.4
- srf_read_index_hdr at Base 1.12.4
- srf_read_pstring at Base 1.12.4
- srf_read_trace_body at Base 1.12.4
- srf_read_trace_hdr at Base 1.12.4
- srf_read_uint32 at Base 1.12.4
- srf_read_uint64 at Base 1.12.4
- srf_read_xml at Base 1.12.4
- srf_write_cont_hdr at Base 1.12.4
- srf_write_index_hdr at Base 1.12.4
- srf_write_pstring at Base 1.12.4
- srf_write_pstringb at Base 1.12.4
- srf_write_trace_body at Base 1.12.4
- srf_write_trace_hdr at Base 1.12.4
- srf_write_uint32 at Base 1.12.4
- srf_write_uint64 at Base 1.12.4
- srf_write_xml at Base 1.12.4
- sthuff at Base 1.12.4
- store_bytes at Base 1.12.4
- store_codes at Base 1.12.4
- store_codes_single at Base 1.12.4
- str2conf at Base 1.12.4
- str2opos at Base 1.12.4
- str_tolower at Base 1.12.4
- str_toupper at Base 1.12.4
- string_alloc at Base 1.13.1
- string_dup at Base 1.13.1
- string_ndup at Base 1.13.1
- string_pool_create at Base 1.13.1
- string_pool_destroy at Base 1.13.1
- stringify_argv at Base 1.13.1
- t_pool_delete_result at Base 1.13.2
- t_pool_destroy at Base 1.13.2
- t_pool_dispatch2 at Base 1.13.2
- t_pool_dispatch at Base 1.13.2
- t_pool_flush at Base 1.13.2
- t_pool_init at Base 1.13.2
- t_pool_next_result at Base 1.13.2
- t_pool_next_result_wait at Base 1.13.2
- t_pool_results_queue_empty at Base 1.13.2
- t_pool_results_queue_len at Base 1.13.2
- t_pool_results_queue_sz at Base 1.13.2
- t_results_queue_destroy at Base 1.13.2
- t_results_queue_init at Base 1.13.2
- tokenise_search_path at Base 1.13.1
- trace_type_int2str at Base 1.12.4
- trace_type_str2int at Base 1.12.4
- trace_type_str at Base 1.12.4
- tshift at Base 1.12.4
- uncompress_chunk at Base 1.12.4
- uncompress_ztr at Base 1.12.4
- unfollow1 at Base 1.12.4
- unlog2_data at Base 1.12.4
- unqshift at Base 1.12.4
- unrle at Base 1.12.4
- unsthuff at Base 1.12.4
- untshift at Base 1.12.4
- unxrle2 at Base 1.12.4
- unxrle at Base 1.12.4
- vflen at Base 1.12.4
- write_abi at Base 1.12.4
- write_alf at Base 1.12.4
-#MISSING: 1.13.3-1# write_ctf at Base 1.12.4
- write_pln at Base 1.12.4
- write_reading at Base 1.12.4
- write_scf at Base 1.12.4
- write_scf_base at Base 1.12.4
- write_scf_bases3 at Base 1.12.4
- write_scf_bases at Base 1.12.4
- write_scf_comment at Base 1.12.4
- write_scf_header at Base 1.12.4
- write_scf_sample1 at Base 1.12.4
- write_scf_sample2 at Base 1.12.4
- write_scf_samples1 at Base 1.12.4
- write_scf_samples2 at Base 1.12.4
- write_scf_samples31 at Base 1.12.4
- write_scf_samples32 at Base 1.12.4
- xcalloc at Base 1.12.4
- xfree at Base 1.12.4
- xmalloc at Base 1.12.4
- xrealloc at Base 1.12.4
- xrle2 at Base 1.12.4
- xrle at Base 1.12.4
- zfclose at Base 1.13.1
- zfeof at Base 1.13.1
- zfgets at Base 1.13.1
- zfopen at Base 1.13.1
- zfpeek at Base 1.13.1
- zfputs at Base 1.13.1
- zfseeko at Base 1.13.1
- zftello at Base 1.13.1
- zlib_dehuff at Base 1.12.4
- zlib_huff at Base 1.12.4
- ztr2read at Base 1.12.4
- ztr_add_hcode at Base 1.12.4
- ztr_add_text at Base 1.12.4
- ztr_dup at Base 1.12.4
- ztr_find_chunks at Base 1.12.4
- ztr_find_hcode at Base 1.12.4
- ztr_find_hcode_chunk at Base 1.12.4
- ztr_lookup_mdata_value at Base 1.12.4
- ztr_new_chunk at Base 1.12.4
- ztr_process_text at Base 1.12.4
- ztr_read_chunk_hdr at Base 1.12.4
- ztr_read_header at Base 1.12.4
- ztr_store_hcodes at Base 1.12.4
Copied: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols (from rev 17245, trunk/packages/staden-io-lib/trunk/debian/libstaden-read1.symbols)
===================================================================
--- trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols (rev 0)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/libstaden-read1.symbols 2014-06-19 23:15:16 UTC (rev 17247)
@@ -0,0 +1,660 @@
+libstaden-read.so.1 libstaden-read1 #MINVER#
+ ArrayCreate at Base 1.12.4
+ ArrayDestroy at Base 1.12.4
+ ArrayError at Base 1.12.4
+ ArrayErrorString at Base 1.12.4
+ ArrayExtend at Base 1.12.4
+ ArrayRef at Base 1.12.4
+ HashFileCreate at Base 1.12.4
+ HashFileDestroy at Base 1.12.4
+ HashFileExtract at Base 1.12.4
+ HashFileFopen at Base 1.12.4
+ HashFileLoad at Base 1.12.4
+ HashFileOpen at Base 1.12.4
+ HashFileQuery at Base 1.12.4
+ HashFileSave at Base 1.12.4
+ HashHsieh at Base 1.12.4
+ HashJenkins3 at Base 1.12.4
+ HashJenkins at Base 1.12.4
+ HashTableAdd at Base 1.12.4
+ HashTableCreate at Base 1.12.4
+ HashTableDel at Base 1.12.4
+ HashTableDestroy at Base 1.12.4
+ HashTableDump at Base 1.12.4
+ HashTableIterCreate at Base 1.12.4
+ HashTableIterDestroy at Base 1.12.4
+ HashTableIterNext at Base 1.12.4
+ HashTableIterReset at Base 1.12.4
+ HashTableNext at Base 1.12.4
+ HashTableNextInt at Base 1.13.7
+ HashTableRemove at Base 1.12.4
+ HashTableResize at Base 1.12.4
+ HashTableSearch at Base 1.12.4
+ HashTableStats at Base 1.12.4
+ HashTcl at Base 1.12.4
+ MD5_Final at Base 1.13.1
+ MD5_Init at Base 1.13.1
+ MD5_Update at Base 1.13.1
+ abi_reset_data_counts at Base 1.12.4
+ abi_set_data_counts at Base 1.12.4
+ arith_compress at Base 1.13.5
+ arith_compress_O0 at Base 1.13.5
+ arith_compress_O1 at Base 1.13.5
+ arith_uncompress at Base 1.13.5
+ arith_uncompress_O0 at Base 1.13.5
+ arith_uncompress_O1 at Base 1.13.5
+ bam_add_raw at Base 1.13.2
+ bam_aux_A at Base 1.13.1
+ bam_aux_Z at Base 1.13.1
+ bam_aux_add at Base 1.13.1
+ bam_aux_add_data at Base 1.13.1
+ bam_aux_add_from_sam at Base 1.13.1
+ bam_aux_add_vec at Base 1.13.1
+ bam_aux_d at Base 1.13.1
+ bam_aux_f at Base 1.13.1
+ bam_aux_find at Base 1.13.1
+ bam_aux_i at Base 1.13.1
+ bam_aux_iter at Base 1.13.1
+ bam_aux_size_vec at Base 1.13.1
+ bam_close at Base 1.13.1
+ bam_construct_seq at Base 1.13.1
+ bam_copy at Base 1.13.2
+ bam_dup at Base 1.13.2
+ bam_get_seq at Base 1.13.1
+ bam_next_seq at Base 1.13.1
+ bam_open at Base 1.13.1
+ bam_put_seq at Base 1.13.1
+ bam_set_option at Base 1.13.2
+ bam_set_voption at Base 1.13.2
+ bam_write_header at Base 1.13.1
+ be_read_int_1 at Base 1.12.4
+ be_read_int_2 at Base 1.12.4
+ be_read_int_4 at Base 1.12.4
+ be_read_int_8 at Base 1.12.4
+ be_write_int_1 at Base 1.12.4
+ be_write_int_2 at Base 1.12.4
+ be_write_int_4 at Base 1.12.4
+ be_write_int_8 at Base 1.12.4
+ bgzf_decode_thread at Base 1.13.2
+ bgzf_encode_thread at Base 1.13.2
+ bit_reverse at Base 1.12.4
+ block_create at Base 1.12.4
+ block_destroy at Base 1.12.4
+ block_resize at Base 1.12.4
+ c2fstr at Base 1.12.4
+ calc_bit_lengths at Base 1.12.4
+ close_fofn at Base 1.12.4
+ codes2codeset at Base 1.12.4
+ compress_chunk at Base 1.12.4
+ compress_file at Base 1.12.4
+ compress_int2str at Base 1.12.4
+ compress_str2int at Base 1.12.4
+ compress_ztr at Base 1.12.4
+ compressed_file_exists at Base 1.12.4
+ conf2str at Base 1.12.4
+ construct_trace_name at Base 1.12.4
+ cram_beta_decode_char at Base 1.13.2
+ cram_beta_decode_free at Base 1.13.1
+ cram_beta_decode_init at Base 1.13.1
+ cram_beta_decode_int at Base 1.13.2
+ cram_beta_encode_char at Base 1.13.1
+ cram_beta_encode_free at Base 1.13.1
+ cram_beta_encode_init at Base 1.13.1
+ cram_beta_encode_int at Base 1.13.1
+ cram_beta_encode_store at Base 1.13.1
+ cram_block_method2str at Base 1.13.1
+ cram_byte_array_len_decode at Base 1.13.1
+ cram_byte_array_len_decode_free at Base 1.13.1
+ cram_byte_array_len_decode_init at Base 1.13.1
+ cram_byte_array_len_encode at Base 1.13.1
+ cram_byte_array_len_encode_free at Base 1.13.1
+ cram_byte_array_len_encode_init at Base 1.13.1
+ cram_byte_array_len_encode_store at Base 1.13.1
+ cram_byte_array_stop_decode_block at Base 1.13.1
+#MISSING: 1.13.7# cram_byte_array_stop_decode_char at Base 1.13.1
+ cram_byte_array_stop_decode_free at Base 1.13.1
+ cram_byte_array_stop_decode_init at Base 1.13.1
+ cram_byte_array_stop_encode at Base 1.13.1
+ cram_byte_array_stop_encode_free at Base 1.13.1
+ cram_byte_array_stop_encode_init at Base 1.13.1
+ cram_byte_array_stop_encode_store at Base 1.13.1
+ cram_close at Base 1.13.1
+ cram_codec_to_id at Base 1.13.7
+ cram_compress_block at Base 1.13.1
+ cram_content_type2str at Base 1.13.1
+ cram_decode_TD at Base 1.13.1
+ cram_decode_compression_header at Base 1.13.1
+ cram_decode_slice at Base 1.13.1
+ cram_decode_slice_header at Base 1.13.1
+ cram_decode_slice_mt at Base 1.13.2
+ cram_decode_slice_thread at Base 1.13.2
+ cram_decoder_init at Base 1.13.1
+ cram_dependent_data_series at Base 1.13.7
+ cram_encode_compression_header at Base 1.13.1
+ cram_encode_container at Base 1.13.1
+ cram_encode_slice_header at Base 1.13.1
+ cram_encoder_init at Base 1.13.1
+ cram_encoding2str at Base 1.13.1
+ cram_eof at Base 1.13.1
+#MISSING: 1.13.7# cram_external_decode_block at Base 1.13.1
+ cram_external_decode_char at Base 1.13.1
+ cram_external_decode_free at Base 1.13.1
+ cram_external_decode_init at Base 1.13.1
+ cram_external_decode_int at Base 1.13.1
+#MISSING: 1.13.7# cram_external_encode at Base 1.13.1
+ cram_external_encode_char at Base 1.13.7
+ cram_external_encode_free at Base 1.13.1
+ cram_external_encode_init at Base 1.13.1
+ cram_external_encode_int at Base 1.13.7
+ cram_external_encode_store at Base 1.13.1
+ cram_flush at Base 1.13.1
+ cram_flush_container at Base 1.13.1
+ cram_flush_container_mt at Base 1.13.2
+ cram_flush_thread at Base 1.13.2
+ cram_free_block at Base 1.13.1
+ cram_free_compression_header at Base 1.13.1
+ cram_free_container at Base 1.13.1
+ cram_free_file_def at Base 1.13.1
+ cram_free_slice at Base 1.13.1
+ cram_free_slice_header at Base 1.13.1
+ cram_gamma_decode at Base 1.13.1
+ cram_gamma_decode_free at Base 1.13.1
+ cram_gamma_decode_init at Base 1.13.1
+ cram_get_bam_seq at Base 1.13.1
+ cram_get_ref at Base 1.13.1
+ cram_get_seq at Base 1.13.1
+ cram_huffman_decode_char0 at Base 1.13.1
+ cram_huffman_decode_char at Base 1.13.1
+ cram_huffman_decode_free at Base 1.13.1
+ cram_huffman_decode_init at Base 1.13.1
+ cram_huffman_decode_int0 at Base 1.13.1
+ cram_huffman_decode_int at Base 1.13.1
+ cram_huffman_encode_char0 at Base 1.13.1
+ cram_huffman_encode_char at Base 1.13.1
+ cram_huffman_encode_free at Base 1.13.1
+ cram_huffman_encode_init at Base 1.13.1
+ cram_huffman_encode_int0 at Base 1.13.1
+ cram_huffman_encode_int at Base 1.13.1
+ cram_huffman_encode_store at Base 1.13.1
+ cram_index_build at Base 1.13.7
+ cram_index_free at Base 1.13.1
+ cram_index_load at Base 1.13.1
+ cram_index_query at Base 1.13.1
+ cram_load_reference at Base 1.13.1
+ cram_new_block at Base 1.13.1
+ cram_new_compression_header at Base 1.13.1
+ cram_new_container at Base 1.13.1
+ cram_new_metrics at Base 1.13.1
+ cram_new_slice at Base 1.13.1
+ cram_open at Base 1.13.1
+ cram_put_bam_seq at Base 1.13.1
+ cram_read_SAM_hdr at Base 1.13.1
+ cram_read_block at Base 1.13.1
+ cram_read_container at Base 1.13.1
+ cram_read_file_def at Base 1.13.1
+ cram_read_slice at Base 1.13.1
+ cram_ref_decr at Base 1.13.2
+ cram_ref_incr at Base 1.13.2
+ cram_ref_load at Base 1.13.2
+ cram_seek at Base 1.13.1
+ cram_seek_to_refpos at Base 1.13.1
+ cram_set_option at Base 1.13.1
+ cram_set_voption at Base 1.13.1
+ cram_stats_add at Base 1.13.1
+ cram_stats_create at Base 1.13.1
+ cram_stats_del at Base 1.13.1
+ cram_stats_dump at Base 1.13.1
+ cram_stats_encoding at Base 1.13.1
+ cram_stats_free at Base 1.13.1
+ cram_subexp_decode at Base 1.13.1
+ cram_subexp_decode_free at Base 1.13.1
+ cram_subexp_decode_init at Base 1.13.1
+ cram_uncompress_block at Base 1.13.1
+ cram_write_SAM_hdr at Base 1.13.1
+ cram_write_block at Base 1.13.1
+ cram_write_container at Base 1.13.1
+ cram_write_file_def at Base 1.13.1
+#MISSING: 1.13.3-1# ctfFRead at Base 1.12.4
+#MISSING: 1.13.3-1# ctfFWrite at Base 1.12.4
+ decode_sff_common_header at Base 1.12.4
+ decode_sff_read_header at Base 1.12.4
+ decorrelate1 at Base 1.12.4
+ decorrelate1dyn at Base 1.12.4
+ decorrelate2 at Base 1.12.4
+ decorrelate2dyn at Base 1.12.4
+ decorrelate4 at Base 1.12.4
+ delete_ztr at Base 1.12.4
+ determine_trace_type at Base 1.12.4
+ dstring_append at Base 1.13.1
+ dstring_append_char at Base 1.13.1
+ dstring_append_hex_encoded at Base 1.13.1
+ dstring_append_int at Base 1.13.1
+ dstring_appendf at Base 1.13.1
+ dstring_create at Base 1.13.1
+ dstring_create_with at Base 1.13.1
+ dstring_delete at Base 1.13.1
+ dstring_destroy at Base 1.13.1
+ dstring_dinsert at Base 1.13.1
+ dstring_dreplace at Base 1.13.1
+ dstring_empty at Base 1.13.1
+ dstring_escape_html at Base 1.13.1
+ dstring_find at Base 1.13.1
+ dstring_find_replace at Base 1.13.1
+ dstring_find_replace_all at Base 1.13.1
+ dstring_htmlise_links at Base 1.13.1
+ dstring_insert at Base 1.13.1
+ dstring_insertf at Base 1.13.1
+ dstring_length at Base 1.13.1
+ dstring_nappend at Base 1.13.1
+ dstring_ninsert at Base 1.13.1
+ dstring_nprepend at Base 1.13.1
+ dstring_perror at Base 1.13.1
+ dstring_prepend at Base 1.13.1
+ dstring_prependf at Base 1.13.1
+ dstring_refresh_length at Base 1.13.1
+ dstring_replace at Base 1.13.1
+ dstring_resize at Base 1.13.1
+ dstring_str at Base 1.13.1
+ dstring_to_html at Base 1.13.1
+ dstring_vinsertf at Base 1.13.1
+ dump_labels at Base 1.12.4
+ eflt_feature_ids at Base 1.12.4
+ encode_sff_common_header at Base 1.12.4
+ encode_sff_read_header at Base 1.12.4
+ errout at Base 1.12.4
+ exp2read at Base 1.12.4
+ exp_close at Base 1.12.4
+ exp_create_info at Base 1.12.4
+ exp_create_range at Base 1.12.4
+ exp_destroy_info at Base 1.12.4
+ exp_extract_range at Base 1.12.4
+ exp_fread_info at Base 1.12.4
+ exp_get_feature_index at Base 1.12.4
+ exp_get_int at Base 1.12.4
+ exp_get_rng at Base 1.12.4
+ exp_get_str at Base 1.12.4
+ exp_mfread_info at Base 1.12.4
+ exp_print_file at Base 1.12.4
+ exp_print_line at Base 1.12.4
+ exp_print_mfile at Base 1.12.4
+ exp_print_mline at Base 1.12.4
+ exp_print_seq at Base 1.12.4
+ exp_put_int at Base 1.12.4
+ exp_put_rng at Base 1.12.4
+ exp_put_str at Base 1.12.4
+ exp_read_info at Base 1.12.4
+ exp_set_entry at Base 1.12.4
+ expand_8to16 at Base 1.12.4
+ expand_8to32 at Base 1.12.4
+ expand_cache_path at Base 1.13.1
+ expcr_ at Base 1.12.4
+ exper_ at Base 1.12.4
+ expkil_ at Base 1.12.4
+ expopn_ at Base 1.12.4
+ expri_ at Base 1.12.4
+ exprr_ at Base 1.12.4
+ exprs_ at Base 1.12.4
+ exprsa_ at Base 1.12.4
+ expwi_ at Base 1.12.4
+ expwr_ at Base 1.12.4
+ expws_ at Base 1.12.4
+ expwsa_ at Base 1.12.4
+ f2cstr at Base 1.12.4
+ fcompress_file at Base 1.12.4
+ fdetermine_trace_type at Base 1.12.4
+ file_exists at Base 1.12.4
+ file_size at Base 1.12.4
+ find_file_url at Base 1.13.1
+ flen at Base 1.12.4
+ follow1 at Base 1.12.4
+ fopen_compressed at Base 1.12.4
+ fread_abi at Base 1.12.4
+ fread_alf at Base 1.12.4
+#MISSING: 1.13.3-1# fread_ctf at Base 1.12.4
+ fread_pln at Base 1.12.4
+ fread_reading at Base 1.12.4
+ fread_scf at Base 1.12.4
+ fread_ztr at Base 1.12.4
+ free_sff_common_header at Base 1.12.4
+ free_sff_read_data at Base 1.12.4
+ free_sff_read_header at Base 1.12.4
+ freopen_compressed at Base 1.12.4
+ fstrlen at Base 1.12.4
+ fwrite_abi at Base 1.12.4
+ fwrite_alf at Base 1.12.4
+#MISSING: 1.13.3-1# fwrite_ctf at Base 1.12.4
+ fwrite_pln at Base 1.12.4
+ fwrite_reading at Base 1.12.4
+ fwrite_scf at Base 1.12.4
+ fwrite_ztr at Base 1.12.4
+ generate_code_set at Base 1.12.4
+ getABIIndexEntryLW at Base 1.12.4
+ getABIIndexEntrySW at Base 1.12.4
+ getABIIndexOffset at Base 1.12.4
+ getABIString at Base 1.12.4
+ getABIint1 at Base 1.12.4
+ getABIint2 at Base 1.12.4
+ getABIint4 at Base 1.12.4
+ get_compression_method at Base 1.12.4
+ get_read_conf at Base 1.12.4
+ hash64 at Base 1.12.4
+ hash at Base 1.12.4
+ huffman_codes_destroy at Base 1.12.4
+ huffman_codeset_destroy at Base 1.12.4
+ huffman_decode at Base 1.12.4
+ huffman_multi_decode at Base 1.12.4
+ huffman_multi_encode at Base 1.12.4
+ ichebcomp at Base 1.12.4
+ ichebuncomp at Base 1.12.4
+ init_decode_tables at Base 1.12.4
+ int32_decode at Base 1.13.1
+ int32_encode at Base 1.13.1
+ int32_get at Base 1.13.1
+ int32_put at Base 1.13.1
+ int_to_float at Base 1.12.4
+ iolib_get_exp_path at Base 1.12.4
+ iolib_get_trace_path at Base 1.12.4
+ iolib_set_exp_path at Base 1.12.4
+ iolib_set_trace_path at Base 1.12.4
+ is_directory at Base 1.12.4
+ is_file at Base 1.12.4
+ is_scf at Base 1.12.4
+ itf8_decode at Base 1.13.1
+ itf8_encode at Base 1.13.1
+ itf8_put_blk at Base 1.13.1
+ le_read_int_1 at Base 1.12.4
+ le_read_int_2 at Base 1.12.4
+ le_read_int_4 at Base 1.12.4
+ le_read_int_8 at Base 1.12.4
+ le_write_int_1 at Base 1.12.4
+ le_write_int_2 at Base 1.12.4
+ le_write_int_4 at Base 1.12.4
+ le_write_int_8 at Base 1.12.4
+ log2_data at Base 1.12.4
+ ltf8_decode at Base 1.13.1
+ ltf8_get at Base 1.13.1
+ ltf8_put at Base 1.13.1
+ memgunzip at Base 1.12.4
+ memgzip at Base 1.12.4
+ mfascii at Base 1.12.4
+ mfclose at Base 1.12.4
+ mfcreate at Base 1.12.4
+ mfcreate_from at Base 1.12.4
+ mfdestroy at Base 1.12.4
+ mfdetach at Base 1.12.4
+ mfeof at Base 1.12.4
+ mfflush at Base 1.12.4
+ mfgetc at Base 1.12.4
+ mfgets at Base 1.12.4
+ mfopen at Base 1.12.4
+ mfprintf at Base 1.12.4
+ mfread at Base 1.12.4
+ mfread_abi at Base 1.12.4
+ mfread_alf at Base 1.12.4
+#MISSING: 1.13.3-1# mfread_ctf at Base 1.12.4
+ mfread_pln at Base 1.12.4
+ mfread_reading at Base 1.12.4
+ mfread_scf at Base 1.12.4
+ mfread_sff at Base 1.12.4
+ mfread_ztr at Base 1.12.4
+ mfrecreate at Base 1.12.4
+ mfreopen at Base 1.12.4
+ mfseek at Base 1.12.4
+ mfsteal at Base 1.13.5
+ mftell at Base 1.12.4
+ mftruncate at Base 1.12.4
+ mfwrite at Base 1.12.4
+ mfwrite_abi at Base 1.12.4
+ mfwrite_alf at Base 1.12.4
+#MISSING: 1.13.3-1# mfwrite_ctf at Base 1.12.4
+ mfwrite_pln at Base 1.12.4
+ mfwrite_reading at Base 1.12.4
+ mfwrite_scf at Base 1.12.4
+ mfwrite_ztr at Base 1.12.4
+ mkdir_prefix at Base 1.13.1
+ mrewind at Base 1.12.4
+ mstderr at Base 1.12.4
+ mstdin at Base 1.12.4
+ mstdout at Base 1.12.4
+ mungetc at Base 1.12.4
+ myfind at Base 1.12.4
+ mystrtok at Base 1.12.4
+ new_ztr at Base 1.12.4
+ next_symbol at Base 1.12.4
+ open_exp_file at Base 1.12.4
+ open_exp_mfile at Base 1.12.4
+ open_fofn at Base 1.12.4
+ open_path_file at Base 1.12.4
+ open_path_mfile at Base 1.12.4
+ open_trace_file at Base 1.12.4
+ open_trace_mfile at Base 1.12.4
+ opos2str at Base 1.12.4
+ pack_trace_suffix at Base 1.12.4
+ paranoid_fclose at Base 1.13.1
+ partial_decode_ztr at Base 1.12.4
+ pool_alloc at Base 1.12.4
+ pool_create at Base 1.12.4
+ pool_destroy at Base 1.12.4
+ pool_free at Base 1.12.4
+ qshift at Base 1.12.4
+ rans_compress at Base 1.13.5
+ rans_compress_O0 at Base 1.13.5
+ rans_compress_O1 at Base 1.13.5
+ rans_uncompress at Base 1.13.5
+ rans_uncompress_O0 at Base 1.13.5
+ rans_uncompress_O1 at Base 1.13.5
+ read2exp at Base 1.12.4
+ read2scf at Base 1.12.4
+ read2ztr at Base 1.12.4
+ read_abi at Base 1.12.4
+ read_alf at Base 1.12.4
+ read_allocate at Base 1.12.4
+#MISSING: 1.13.3-1# read_ctf at Base 1.12.4
+ read_deallocate at Base 1.12.4
+ read_dup at Base 1.12.4
+ read_experiment_redirect at Base 1.12.4
+ read_fofn at Base 1.12.4
+ read_pln at Base 1.12.4
+ read_reading at Base 1.12.4
+ read_scf at Base 1.12.4
+ read_scf_base at Base 1.12.4
+ read_scf_bases3 at Base 1.12.4
+ read_scf_bases at Base 1.12.4
+ read_scf_comment at Base 1.12.4
+ read_scf_header at Base 1.12.4
+ read_scf_sample1 at Base 1.12.4
+ read_scf_sample2 at Base 1.12.4
+ read_scf_samples1 at Base 1.12.4
+ read_scf_samples2 at Base 1.12.4
+ read_scf_samples31 at Base 1.12.4
+ read_scf_samples32 at Base 1.12.4
+ read_sections at Base 1.12.4
+ read_sff_common_header at Base 1.12.4
+ read_sff_read_data at Base 1.12.4
+ read_sff_read_header at Base 1.12.4
+ read_update_base_positions at Base 1.12.4
+ read_update_confidence_values at Base 1.12.4
+ recorrelate1 at Base 1.12.4
+ recorrelate2 at Base 1.12.4
+ recorrelate4 at Base 1.12.4
+ refs2id at Base 1.13.1
+ refs_free at Base 1.13.2
+ remove_extension at Base 1.12.4
+ remove_file at Base 1.12.4
+ restore_codes at Base 1.12.4
+ restore_codes_single at Base 1.12.4
+ rle at Base 1.12.4
+ sam_hdr_PG_ID at Base 1.13.1
+ sam_hdr_add at Base 1.13.1
+ sam_hdr_add_PG at Base 1.13.1
+ sam_hdr_add_lines at Base 1.13.1
+ sam_hdr_decr_ref at Base 1.13.2
+ sam_hdr_dump at Base 1.13.1
+ sam_hdr_dup at Base 1.13.1
+ sam_hdr_find at Base 1.13.1
+ sam_hdr_find_key at Base 1.13.1
+ sam_hdr_find_line at Base 1.13.1
+ sam_hdr_find_rg at Base 1.13.1
+ sam_hdr_free at Base 1.13.1
+ sam_hdr_incr_ref at Base 1.13.2
+ sam_hdr_length at Base 1.13.1
+ sam_hdr_link_pg at Base 1.13.1
+ sam_hdr_name2ref at Base 1.13.1
+ sam_hdr_new at Base 1.13.1
+ sam_hdr_parse at Base 1.13.1
+ sam_hdr_rebuild at Base 1.13.1
+ sam_hdr_str at Base 1.13.1
+ sam_hdr_update at Base 1.13.1
+ sam_hdr_vadd at Base 1.13.1
+ scf2read at Base 1.12.4
+ scf_allocate at Base 1.12.4
+ scf_deallocate at Base 1.12.4
+ scf_delta_samples1 at Base 1.12.4
+ scf_delta_samples2 at Base 1.12.4
+ scf_version_float2str at Base 1.12.4
+ scf_version_str2float at Base 1.12.4
+ scram_close at Base 1.13.1
+ scram_get_header at Base 1.13.1
+ scram_get_refs at Base 1.13.1
+ scram_get_seq at Base 1.13.1
+ scram_input_bam_block at Base 1.13.2
+ scram_line at Base 1.13.2
+ scram_next_seq at Base 1.13.1
+ scram_open at Base 1.13.1
+ scram_put_seq at Base 1.13.1
+ scram_set_header at Base 1.13.1
+ scram_set_option at Base 1.13.1
+ scram_set_refs at Base 1.13.1
+ scram_write_header at Base 1.13.1
+ set_compression_method at Base 1.12.4
+ set_scf_version at Base 1.12.4
+ shrink_16to8 at Base 1.12.4
+ shrink_32to8 at Base 1.12.4
+ srf_construct_cont_hdr at Base 1.12.4
+ srf_construct_trace_body at Base 1.12.4
+ srf_construct_trace_hdr at Base 1.12.4
+ srf_create at Base 1.12.4
+ srf_destroy at Base 1.12.4
+ srf_destroy_cont_hdr at Base 1.12.4
+ srf_destroy_trace_body at Base 1.12.4
+ srf_destroy_trace_hdr at Base 1.12.4
+ srf_find_trace at Base 1.12.4
+ srf_index_add_cont_hdr at Base 1.12.4
+ srf_index_add_trace_body at Base 1.12.4
+ srf_index_add_trace_hdr at Base 1.12.4
+ srf_index_create at Base 1.12.4
+ srf_index_destroy at Base 1.12.4
+ srf_index_stats at Base 1.12.4
+ srf_index_write at Base 1.12.4
+ srf_next_block_details at Base 1.12.4
+ srf_next_block_type at Base 1.12.4
+ srf_next_trace at Base 1.12.4
+ srf_next_ztr at Base 1.12.4
+ srf_next_ztr_flags at Base 1.12.4
+ srf_open at Base 1.12.4
+ srf_read_cont_hdr at Base 1.12.4
+ srf_read_index_hdr at Base 1.12.4
+ srf_read_pstring at Base 1.12.4
+ srf_read_trace_body at Base 1.12.4
+ srf_read_trace_hdr at Base 1.12.4
+ srf_read_uint32 at Base 1.12.4
+ srf_read_uint64 at Base 1.12.4
+ srf_read_xml at Base 1.12.4
+ srf_write_cont_hdr at Base 1.12.4
+ srf_write_index_hdr at Base 1.12.4
+ srf_write_pstring at Base 1.12.4
+ srf_write_pstringb at Base 1.12.4
+ srf_write_trace_body at Base 1.12.4
+ srf_write_trace_hdr at Base 1.12.4
+ srf_write_uint32 at Base 1.12.4
+ srf_write_uint64 at Base 1.12.4
+ srf_write_xml at Base 1.12.4
+ sthuff at Base 1.12.4
+ store_bytes at Base 1.12.4
+ store_codes at Base 1.12.4
+ store_codes_single at Base 1.12.4
+ str2conf at Base 1.12.4
+ str2opos at Base 1.12.4
+ str_tolower at Base 1.12.4
+ str_toupper at Base 1.12.4
+ string_alloc at Base 1.13.1
+ string_dup at Base 1.13.1
+ string_ndup at Base 1.13.1
+ string_pool_create at Base 1.13.1
+ string_pool_destroy at Base 1.13.1
+ stringify_argv at Base 1.13.1
+ t_pool_delete_result at Base 1.13.2
+ t_pool_destroy at Base 1.13.2
+ t_pool_dispatch2 at Base 1.13.2
+ t_pool_dispatch at Base 1.13.2
+ t_pool_flush at Base 1.13.2
+ t_pool_init at Base 1.13.2
+ t_pool_next_result at Base 1.13.2
+ t_pool_next_result_wait at Base 1.13.2
+ t_pool_results_queue_empty at Base 1.13.2
+ t_pool_results_queue_len at Base 1.13.2
+ t_pool_results_queue_sz at Base 1.13.2
+ t_results_queue_destroy at Base 1.13.2
+ t_results_queue_init at Base 1.13.2
+ tokenise_search_path at Base 1.13.1
+ trace_type_int2str at Base 1.12.4
+ trace_type_str2int at Base 1.12.4
+ trace_type_str at Base 1.12.4
+ tshift at Base 1.12.4
+ uncompress_chunk at Base 1.12.4
+ uncompress_ztr at Base 1.12.4
+ unfollow1 at Base 1.12.4
+ unlog2_data at Base 1.12.4
+ unqshift at Base 1.12.4
+ unrle at Base 1.12.4
+ unsthuff at Base 1.12.4
+ untshift at Base 1.12.4
+ unxrle2 at Base 1.12.4
+ unxrle at Base 1.12.4
+ vflen at Base 1.12.4
+ write_abi at Base 1.12.4
+ write_alf at Base 1.12.4
+#MISSING: 1.13.3-1# write_ctf at Base 1.12.4
+ write_pln at Base 1.12.4
+ write_reading at Base 1.12.4
+ write_scf at Base 1.12.4
+ write_scf_base at Base 1.12.4
+ write_scf_bases3 at Base 1.12.4
+ write_scf_bases at Base 1.12.4
+ write_scf_comment at Base 1.12.4
+ write_scf_header at Base 1.12.4
+ write_scf_sample1 at Base 1.12.4
+ write_scf_sample2 at Base 1.12.4
+ write_scf_samples1 at Base 1.12.4
+ write_scf_samples2 at Base 1.12.4
+ write_scf_samples31 at Base 1.12.4
+ write_scf_samples32 at Base 1.12.4
+ xcalloc at Base 1.12.4
+ xfree at Base 1.12.4
+ xmalloc at Base 1.12.4
+ xrealloc at Base 1.12.4
+ xrle2 at Base 1.12.4
+ xrle at Base 1.12.4
+ zfclose at Base 1.13.1
+ zfeof at Base 1.13.1
+ zfgets at Base 1.13.1
+ zfopen at Base 1.13.1
+ zfpeek at Base 1.13.1
+ zfputs at Base 1.13.1
+ zfseeko at Base 1.13.1
+ zftello at Base 1.13.1
+ zlib_dehuff at Base 1.12.4
+ zlib_huff at Base 1.12.4
+ ztr2read at Base 1.12.4
+ ztr_add_hcode at Base 1.12.4
+ ztr_add_text at Base 1.12.4
+ ztr_dup at Base 1.12.4
+ ztr_find_chunks at Base 1.12.4
+ ztr_find_hcode at Base 1.12.4
+ ztr_find_hcode_chunk at Base 1.12.4
+ ztr_lookup_mdata_value at Base 1.12.4
+ ztr_new_chunk at Base 1.12.4
+ ztr_process_text at Base 1.12.4
+ ztr_read_chunk_hdr at Base 1.12.4
+ ztr_read_header at Base 1.12.4
+ ztr_store_hcodes at Base 1.12.4
Deleted: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/fix-bam-read.patch
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/patches/fix-bam-read.patch 2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/fix-bam-read.patch 2014-06-19 23:15:16 UTC (rev 17247)
@@ -1,36 +0,0 @@
-Date: Mon, 31 Mar 2014 19:22:13 +0200
-From: Aleksandar Zlicic <Aleksandar.Zlicic at imgtec.com>
-Subject: staden-io-lib: fix io_lib/bam.c read
-
-https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565
-
-We have fixed a bug reported for the staden-io-lib package
-(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565). The cause
-of this problem is an error in function bam_get_seq(), or to be more
-precise, function's implementation for non-intel architectures.
-
-Function bam_get_seq is used for reading data from alignment blocks in
-BAM files, block by block.
-
-In special cases, when the alignment block being read is the last
-block in BAM file, and the block has no cigar operations and segment
-sequence stored inside of it, function incorrectly detects
-end-of-file.
-
-In that case, block has actually been successfully read, but because
-of erroneous end-of-file detection, it isn't written to output file in
-SAM format.
-
-Attached patch fixes this issue.
-
---- a/io_lib/bam.c 2014-01-07 17:01:12.000000000 +0000
-+++ bio_lib//bam.c 2014-04-01 04:05:16.762660873 +0100
-@@ -1635,7 +1635,7 @@ int bam_get_seq(bam_file_t *b, bam_seq_t
-
- /* The remainder, word aligned */
- blk_size = blk_ret;
-- if ((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0)
-+ if (((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0) && blk_size != 0)
- return 0;
- if (blk_size+4 != blk_ret) {
- if (blk_size != blk_ret) {
Deleted: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/patches/series 2014-06-18 15:22:25 UTC (rev 17219)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series 2014-06-19 23:15:16 UTC (rev 17247)
@@ -1,2 +0,0 @@
-pathmax.patch
-fix-bam-read.patch
Copied: trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series (from rev 17220, trunk/packages/staden-io-lib/trunk/debian/patches/series)
===================================================================
--- trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series (rev 0)
+++ trunk/packages/staden-io-lib/tags/1.13.7-1/debian/patches/series 2014-06-19 23:15:16 UTC (rev 17247)
@@ -0,0 +1 @@
+pathmax.patch
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