debian/0000755000000000000000000000000012263727311007172 5ustar debian/source/0000755000000000000000000000000012263727307010477 5ustar debian/source/format0000644000000000000000000000001412165743656011713 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000216512165743656011144 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: squizz Source: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz Files-Excluded: test/sequence/sprot.seq Files: * Copyright: 2011 Nicolas Joly License: GPL-2+ Files: debian/* Copyright: 2011 Olivier Sallou License: GPL-2+ License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/squizz.manpages0000644000000000000000000000001712165743656012265 0ustar doc/squizz.man debian/compat0000644000000000000000000000000212165743656010403 0ustar 9 debian/README.source0000644000000000000000000000054012165743656011363 0ustar Default source includes a test data file with incompatible license. To work around this, one should use the get-orig-source command to update the source which will remove the involved file. A patch is also required to remove from build step the tests using this data file. -- Olivier Sallou Mon, 21 Mar 2011 15:32:00 +0100 debian/watch0000644000000000000000000000020012165743656010226 0ustar version=3 opts=passive,dversionmangle=s/[~\+]dfsg// \ ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/squizz-(.*)\.tar\.gz debian/docs0000644000000000000000000000002112165743656010051 0ustar NEWS README TODO debian/libsquizz-dev.install0000644000000000000000000000015312165743656013404 0ustar debian/tmp/usr/lib/*/*.a usr/lib/ debian/tmp/usr/include/* usr/include debian/tmp/usr/lib/*/*.so usr/lib/ debian/libsquizz.install0000644000000000000000000000005112165743656012625 0ustar debian/tmp/usr/lib/*/lib*.so.* usr/lib/ debian/patches/0000755000000000000000000000000012263727307010626 5ustar debian/patches/disable-swissprot-test.patch0000644000000000000000000000555312165743656016320 0ustar Subject: Disable tests using copyrigthed seq Description: upstream constains copyrighted sequence, removed form packaged. This patch removes tests using this sequence Author: Olivier Sallou Last-Updated: 2013-02-18 Forwarded: No --- a/test/Makefile.am +++ b/test/Makefile.am @@ -6,7 +6,7 @@ TESTS_ALIS = clustal.sh mega.sh msf.sh nexusi.sh phylipi.sh phylips.sh \ stockholm.sh -TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh sprot.sh +TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh XFAIL_TESTS = @@ -18,6 +18,6 @@ SEQS = sequence/embl.seq sequence/fasta.seq sequence/gde.seq \ sequence/genbank.seq sequence/genpept.seq sequence/gcg.seq \ sequence/ig.seq sequence/nbrf.seq sequence/codata.seq sequence/raw.seq \ - sequence/refseqn.seq sequence/refseqp.seq sequence/sprot.seq + sequence/refseqn.seq sequence/refseqp.seq EXTRA_DIST = $(TESTS) $(DATAS) --- a/test/Makefile.in +++ b/test/Makefile.in @@ -417,7 +417,7 @@ TESTS_ALIS = clustal.sh mega.sh msf.sh nexusi.sh phylipi.sh phylips.sh \ stockholm.sh -TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh sprot.sh +TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh DATAS = $(ALIS) $(SEQS) ALIS = align/clustal.seq align/fasta.seq align/mega.seq align/msf.seq \ align/nexusi.seq align/phylipi.seq align/phylips.seq align/stock.seq @@ -425,7 +425,7 @@ SEQS = sequence/embl.seq sequence/fasta.seq sequence/gde.seq \ sequence/genbank.seq sequence/genpept.seq sequence/gcg.seq \ sequence/ig.seq sequence/nbrf.seq sequence/codata.seq sequence/raw.seq \ - sequence/refseqn.seq sequence/refseqp.seq sequence/sprot.seq + sequence/refseqn.seq sequence/refseqp.seq EXTRA_DIST = $(TESTS) $(DATAS) all: all-am --- a/test/convseq.sh +++ b/test/convseq.sh @@ -7,7 +7,7 @@ ## Sequence files location seqdir=$srcdir/sequence -seqlist='codata.seq embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq nbrf.seq raw.seq refseqn.seq refseqp.seq sprot.seq' +seqlist='codata.seq embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq nbrf.seq raw.seq refseqn.seq refseqp.seq' ## Checks CODATA-like sequence for f in $seqlist; do @@ -64,10 +64,10 @@ done ## Checks SWISSPROT-like sequence -for f in $seqlist; do - ../src/squizz -c swissprot $seqdir/$f >$tmpseq 2>/dev/null - (../src/squizz $tmpseq 2>&1 | grep -v SWISSPROT) && exit 1 -done +#for f in $seqlist; do +# ../src/squizz -c swissprot $seqdir/$f >$tmpseq 2>/dev/null +# (../src/squizz $tmpseq 2>&1 | grep -v SWISSPROT) && exit 1 +#done ## Clean temp files rm -f $tmpseq --- a/test/fmtseq.sh +++ b/test/fmtseq.sh @@ -61,10 +61,10 @@ done ## Checks SWISSPROT-like sequence -seqlist='sprot.seq' -for f in $seqlist; do - (../src/squizz $srcdir/$f 2>&1 | grep -v SWISSPROT) && exit 1 -done +#seqlist='sprot.seq' +#for f in $seqlist; do +# (../src/squizz $srcdir/$f 2>&1 | grep -v SWISSPROT) && exit 1 +#done exit 0 debian/patches/series0000644000000000000000000000007412165743656012052 0ustar correct-manpages-section.patch disable-swissprot-test.patch debian/patches/correct-manpages-section.patch0000644000000000000000000000177112165743656016557 0ustar Subject: Fix man page section Description: wrong section used Author: Olivier Sallou Last-Updated: 2013-02-18 Forwarded: Yes --- a/doc/alifmt.man +++ b/doc/alifmt.man @@ -128,8 +128,8 @@ .rm #[ #] #H #V #F C .\" ======================================================================== .\" -.IX Title "ALIFMT 1" -.TH ALIFMT 1 "2009-05-19" "Unix" "User Manuals" +.IX Title "ALIFMT 5" +.TH ALIFMT 5 "2009-05-19" "Unix" "User Manuals" .SH "NAME" .IP "\fBalifmt\fR \- Aligned sequences formats" 4 .IX Item "alifmt - Aligned sequences formats" --- a/doc/seqfmt.man +++ b/doc/seqfmt.man @@ -123,8 +123,8 @@ .rm #[ #] #H #V #F C .\" ======================================================================== .\" -.IX Title "SEQFMT 1" -.TH SEQFMT 1 "2013-02-08" "Unix" "User Manuals" +.IX Title "SEQFMT 5" +.TH SEQFMT 5 "2013-02-08" "Unix" "User Manuals" .\" For nroff, turn off justification. Always turn off hyphenation; it makes .\" way too many mistakes in technical documents. .if n .ad l debian/get-orig-source0000644000000000000000000000133212165743656012142 0ustar #!/bin/bash set -e PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` VERSION=`uscan --verbose --force-download | grep "Newest version on remote site is .* local version is .*" | head -n 1 | sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"` mkdir -p ../tarballs cd ../tarballs #UTAR="${PKG}_${VERSION}.orig.tar.gz" UTAR="${PKG}-${VERSION}.tar.gz" mv ../${UTAR} . tar -xzf ${UTAR} mv $PKG-${VERSION} $PKG-${VERSION}+dfsg.orig # Requested by Developers Reference 3.4.4 §6.7.8.2 cd $PKG-${VERSION}+dfsg.orig rm -f test/sequence/sprot.seq cd .. rm $UTAR GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION"+dfsg.orig.tar.gz "${PKG}-${VERSION}+dfsg.orig" rm -rf "${PKG}-${VERSION}+dfsg.orig" debian/control0000644000000000000000000000422312263727244010603 0ustar Source: squizz Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou , Andreas Tille Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/squizz/trunk/ Vcs-Browser: http://anonscm.debian.org/svn/debian-med/trunk/packages/squizz/trunk/ Homepage: ftp://ftp.pasteur.fr/pub/gensoft/projects/squizz/ Build-Depends: debhelper (>= 9), dh-autoreconf Standards-Version: 3.9.4 Package: squizz Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Breaks: squizz (<=0.99a) Description: Converter for genetic sequences and alignments Squizz is a sequence/alignment format checker, but it has some conversion capabilities too. Most common sequence and alignment formats are supported : - EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT. - CLUSTAL, FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM. Package: libsquizz Architecture: any Section: libs Depends: ${shlibs:Depends}, ${misc:Depends} Breaks: squizz (<=0.99a) Description: Conversion libs used by squizz genetic sequence converter Squizz is a sequence/alignment format checker, but it has some conversion capabilities too. Most common sequence and alignment formats are supported : - EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT. - CLUSTAL, FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM. . This package provides required libs for squizz binary Package: libsquizz-dev Section: libdevel Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, libsquizz Breaks: squizz (<=0.99a) Description: development tools for squizz genetic sequence converter Squizz is a sequence/alignment format checker, but it has some conversion capabilities too. Most common sequence and alignment formats are supported : - EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT. - CLUSTAL, FASTA, MEGA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM. . This package provides the required static libs and header files of squizz debian/rules0000755000000000000000000000041212263727214010251 0ustar #!/usr/bin/make -f # debian/rules file for squizz #export DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 %: dh $@ --with autoreconf get-orig-source: . debian/get-orig-source debian/libsquizz.symbols0000644000000000000000000004627612165743656012672 0ustar libbioali.so.0 libsquizz #MINVER# align_check@Base 0.99a align_format@Base 0.99a align_free@Base 0.99a align_new@Base 0.99a align_parse@Base 0.99a align_print@Base 0.99a align_strict@Base 0.99a clustal_check@Base 0.99a clustal_conserv@Base 0.99a clustal_create_buffer@Base 0.99a clustal_delete_buffer@Base 0.99a clustal_flex_debug@Base 0.99a clustal_flush_buffer@Base 0.99a clustal_parse@Base 0.99a clustal_print@Base 0.99a clustal_scan_buffer@Base 0.99a clustal_scan_bytes@Base 0.99a clustal_scan_string@Base 0.99a clustal_switch_to_buffer@Base 0.99a clustalalloc@Base 0.99a clustalfree@Base 0.99a clustalget_debug@Base 0.99a clustalget_in@Base 0.99a clustalget_leng@Base 0.99a clustalget_lineno@Base 0.99a clustalget_out@Base 0.99a clustalget_text@Base 0.99a clustalin@Base 0.99a clustalleng@Base 0.99a clustallex@Base 0.99a clustallex_destroy@Base 0.99a clustallineno@Base 0.99a clustalout@Base 0.99a clustalparse@Base 0.99a clustalpop_buffer_state@Base 0.99a clustalpush_buffer_state@Base 0.99a clustalrealloc@Base 0.99a clustalrestart@Base 0.99a clustalset_debug@Base 0.99a clustalset_in@Base 0.99a clustalset_lineno@Base 0.99a clustalset_out@Base 0.99a clustaltext@Base 0.99a clustaly_check@Base 0.99a clustaly_parse@Base 0.99a fasta2_check@Base 0.99a fasta2_parse@Base 0.99a fasta2_print@Base 0.99a mega_check@Base 0.99a mega_create_buffer@Base 0.99a mega_delete_buffer@Base 0.99a mega_flex_debug@Base 0.99a mega_flush_buffer@Base 0.99a mega_parse@Base 0.99a mega_print@Base 0.99a mega_scan_buffer@Base 0.99a mega_scan_bytes@Base 0.99a mega_scan_string@Base 0.99a mega_switch_to_buffer@Base 0.99a megaalloc@Base 0.99a megafree@Base 0.99a megaget_debug@Base 0.99a megaget_in@Base 0.99a megaget_leng@Base 0.99a megaget_lineno@Base 0.99a megaget_out@Base 0.99a megaget_text@Base 0.99a megain@Base 0.99a megaleng@Base 0.99a megalex@Base 0.99a megalex_destroy@Base 0.99a megalineno@Base 0.99a megaout@Base 0.99a megaparse@Base 0.99a megapop_buffer_state@Base 0.99a megapush_buffer_state@Base 0.99a megarealloc@Base 0.99a megarestart@Base 0.99a megaset_debug@Base 0.99a megaset_in@Base 0.99a megaset_lineno@Base 0.99a megaset_out@Base 0.99a megatext@Base 0.99a megay_check@Base 0.99a megay_parse@Base 0.99a msf_check@Base 0.99a msf_crc@Base 0.99a msf_create_buffer@Base 0.99a msf_delete_buffer@Base 0.99a msf_flex_debug@Base 0.99a msf_flush_buffer@Base 0.99a msf_parse@Base 0.99a msf_print@Base 0.99a msf_scan_buffer@Base 0.99a msf_scan_bytes@Base 0.99a msf_scan_string@Base 0.99a msf_switch_to_buffer@Base 0.99a msfalloc@Base 0.99a msffree@Base 0.99a msfget_debug@Base 0.99a msfget_in@Base 0.99a msfget_leng@Base 0.99a msfget_lineno@Base 0.99a msfget_out@Base 0.99a msfget_text@Base 0.99a msfin@Base 0.99a msfleng@Base 0.99a msflex@Base 0.99a msflex_destroy@Base 0.99a msflineno@Base 0.99a msfout@Base 0.99a msfparse@Base 0.99a msfpop_buffer_state@Base 0.99a msfpush_buffer_state@Base 0.99a msfrealloc@Base 0.99a msfrestart@Base 0.99a msfset_debug@Base 0.99a msfset_in@Base 0.99a msfset_lineno@Base 0.99a msfset_out@Base 0.99a msftext@Base 0.99a msfy_check@Base 0.99a msfy_parse@Base 0.99a nexusi_check@Base 0.99a nexusi_create_buffer@Base 0.99a nexusi_delete_buffer@Base 0.99a nexusi_flex_debug@Base 0.99a nexusi_flush_buffer@Base 0.99a nexusi_parse@Base 0.99a nexusi_print@Base 0.99a nexusi_scan_buffer@Base 0.99a nexusi_scan_bytes@Base 0.99a nexusi_scan_string@Base 0.99a nexusi_switch_to_buffer@Base 0.99a nexusialloc@Base 0.99a nexusifree@Base 0.99a nexusiget_debug@Base 0.99a nexusiget_in@Base 0.99a nexusiget_leng@Base 0.99a nexusiget_lineno@Base 0.99a nexusiget_out@Base 0.99a nexusiget_text@Base 0.99a nexusiin@Base 0.99a nexusileng@Base 0.99a nexusilex@Base 0.99a nexusilex_destroy@Base 0.99a nexusilineno@Base 0.99a nexusiout@Base 0.99a nexusiparse@Base 0.99a nexusipop_buffer_state@Base 0.99a nexusipush_buffer_state@Base 0.99a nexusirealloc@Base 0.99a nexusirestart@Base 0.99a nexusiset_debug@Base 0.99a nexusiset_in@Base 0.99a nexusiset_lineno@Base 0.99a nexusiset_out@Base 0.99a nexusitext@Base 0.99a nexusiy_check@Base 0.99a nexusiy_parse@Base 0.99a parse_seqnew@Base 0.99a parse_seqnxt@Base 0.99a parse_seqrst@Base 0.99a parse_sequpd@Base 0.99a parse_tmpupd@Base 0.99a phylip_fixnam@Base 0.99a phylipi_check@Base 0.99a phylipi_create_buffer@Base 0.99a phylipi_delete_buffer@Base 0.99a phylipi_flex_debug@Base 0.99a phylipi_flush_buffer@Base 0.99a phylipi_parse@Base 0.99a phylipi_print@Base 0.99a phylipi_scan_buffer@Base 0.99a phylipi_scan_bytes@Base 0.99a phylipi_scan_string@Base 0.99a phylipi_switch_to_buffer@Base 0.99a phylipialloc@Base 0.99a phylipifree@Base 0.99a phylipiget_debug@Base 0.99a phylipiget_in@Base 0.99a phylipiget_leng@Base 0.99a phylipiget_lineno@Base 0.99a phylipiget_out@Base 0.99a phylipiget_text@Base 0.99a phylipiin@Base 0.99a phylipileng@Base 0.99a phylipilex@Base 0.99a phylipilex_destroy@Base 0.99a phylipilineno@Base 0.99a phylipiout@Base 0.99a phylipiparse@Base 0.99a phylipipop_buffer_state@Base 0.99a phylipipush_buffer_state@Base 0.99a phylipirealloc@Base 0.99a phylipirestart@Base 0.99a phylipiset_debug@Base 0.99a phylipiset_in@Base 0.99a phylipiset_lineno@Base 0.99a phylipiset_out@Base 0.99a phylipitext@Base 0.99a phylipiy_check@Base 0.99a phylipiy_parse@Base 0.99a phylips_check@Base 0.99a phylips_create_buffer@Base 0.99a phylips_delete_buffer@Base 0.99a phylips_flex_debug@Base 0.99a phylips_flush_buffer@Base 0.99a phylips_parse@Base 0.99a phylips_print@Base 0.99a phylips_scan_buffer@Base 0.99a phylips_scan_bytes@Base 0.99a phylips_scan_string@Base 0.99a phylips_switch_to_buffer@Base 0.99a phylipsalloc@Base 0.99a phylipsfree@Base 0.99a phylipsget_debug@Base 0.99a phylipsget_in@Base 0.99a phylipsget_leng@Base 0.99a phylipsget_lineno@Base 0.99a phylipsget_out@Base 0.99a phylipsget_text@Base 0.99a phylipsin@Base 0.99a phylipsleng@Base 0.99a phylipslex@Base 0.99a phylipslex_destroy@Base 0.99a phylipslineno@Base 0.99a phylipsout@Base 0.99a phylipsparse@Base 0.99a phylipspop_buffer_state@Base 0.99a phylipspush_buffer_state@Base 0.99a phylipsrealloc@Base 0.99a phylipsrestart@Base 0.99a phylipsset_debug@Base 0.99a phylipsset_in@Base 0.99a phylipsset_lineno@Base 0.99a phylipsset_out@Base 0.99a phylipstext@Base 0.99a phylipsy_check@Base 0.99a phylipsy_parse@Base 0.99a stock_check@Base 0.99a stock_create_buffer@Base 0.99a stock_delete_buffer@Base 0.99a stock_flex_debug@Base 0.99a stock_flush_buffer@Base 0.99a stock_parse@Base 0.99a stock_print@Base 0.99a stock_scan_buffer@Base 0.99a stock_scan_bytes@Base 0.99a stock_scan_string@Base 0.99a stock_switch_to_buffer@Base 0.99a stockalloc@Base 0.99a stockfree@Base 0.99a stockget_debug@Base 0.99a stockget_in@Base 0.99a stockget_leng@Base 0.99a stockget_lineno@Base 0.99a stockget_out@Base 0.99a stockget_text@Base 0.99a stockin@Base 0.99a stockleng@Base 0.99a stocklex@Base 0.99a stocklex_destroy@Base 0.99a stocklineno@Base 0.99a stockout@Base 0.99a stockparse@Base 0.99a stockpop_buffer_state@Base 0.99a stockpush_buffer_state@Base 0.99a stockrealloc@Base 0.99a stockrestart@Base 0.99a stockset_debug@Base 0.99a stockset_in@Base 0.99a stockset_lineno@Base 0.99a stockset_out@Base 0.99a stocktext@Base 0.99a stocky_check@Base 0.99a stocky_parse@Base 0.99a libbioseq.so.0 libsquizz #MINVER# codata_check@Base 0.99b+dfsg codata_checksum@Base 0.99b+dfsg codata_create_buffer@Base 0.99b+dfsg codata_delete_buffer@Base 0.99b+dfsg codata_flex_debug@Base 0.99b+dfsg codata_flush_buffer@Base 0.99b+dfsg codata_parse@Base 0.99b+dfsg codata_print@Base 0.99b+dfsg codata_scan_buffer@Base 0.99b+dfsg codata_scan_bytes@Base 0.99b+dfsg codata_scan_string@Base 0.99b+dfsg codata_switch_to_buffer@Base 0.99b+dfsg codataalloc@Base 0.99b+dfsg codatafree@Base 0.99b+dfsg codataget_debug@Base 0.99b+dfsg codataget_in@Base 0.99b+dfsg codataget_leng@Base 0.99b+dfsg codataget_lineno@Base 0.99b+dfsg codataget_out@Base 0.99b+dfsg codataget_text@Base 0.99b+dfsg codatain@Base 0.99b+dfsg codataleng@Base 0.99b+dfsg codatalex@Base 0.99b+dfsg codatalex_destroy@Base 0.99b+dfsg codatalineno@Base 0.99b+dfsg codataout@Base 0.99b+dfsg codataparse@Base 0.99b+dfsg codatapop_buffer_state@Base 0.99b+dfsg codatapush_buffer_state@Base 0.99b+dfsg codatarealloc@Base 0.99b+dfsg codatarestart@Base 0.99b+dfsg codataset_debug@Base 0.99b+dfsg codataset_in@Base 0.99b+dfsg codataset_lineno@Base 0.99b+dfsg codataset_out@Base 0.99b+dfsg codatatext@Base 0.99b+dfsg codatay_check@Base 0.99b+dfsg codatay_parse@Base 0.99b+dfsg embl_check@Base 0.99a embl_create_buffer@Base 0.99a embl_delete_buffer@Base 0.99a embl_flex_debug@Base 0.99a embl_flush_buffer@Base 0.99a embl_parse@Base 0.99a embl_print@Base 0.99a embl_scan_buffer@Base 0.99a embl_scan_bytes@Base 0.99a embl_scan_string@Base 0.99a embl_switch_to_buffer@Base 0.99a emblalloc@Base 0.99a emblfree@Base 0.99a emblget_debug@Base 0.99a emblget_in@Base 0.99a emblget_leng@Base 0.99a emblget_lineno@Base 0.99a emblget_out@Base 0.99a emblget_text@Base 0.99a emblin@Base 0.99a emblleng@Base 0.99a embllex@Base 0.99a embllex_destroy@Base 0.99a embllineno@Base 0.99a emblout@Base 0.99a emblparse@Base 0.99a emblpop_buffer_state@Base 0.99a emblpush_buffer_state@Base 0.99a emblrealloc@Base 0.99a emblrestart@Base 0.99a emblset_debug@Base 0.99a emblset_in@Base 0.99a emblset_lineno@Base 0.99a emblset_out@Base 0.99a embltext@Base 0.99a embly_check@Base 0.99a embly_parse@Base 0.99a #MISSING: 0.99b+dfsg# error_fatal@Base 0.99a #MISSING: 0.99b+dfsg# error_warn@Base 0.99a fasta_check@Base 0.99a fasta_create_buffer@Base 0.99a fasta_delete_buffer@Base 0.99a fasta_flex_debug@Base 0.99a fasta_flush_buffer@Base 0.99a fasta_parse@Base 0.99a fasta_print@Base 0.99a fasta_scan_buffer@Base 0.99a fasta_scan_bytes@Base 0.99a fasta_scan_string@Base 0.99a fasta_switch_to_buffer@Base 0.99a fastaalloc@Base 0.99a fastafree@Base 0.99a fastaget_debug@Base 0.99a fastaget_in@Base 0.99a fastaget_leng@Base 0.99a fastaget_lineno@Base 0.99a fastaget_out@Base 0.99a fastaget_text@Base 0.99a fastain@Base 0.99a fastaleng@Base 0.99a fastalex@Base 0.99a fastalex_destroy@Base 0.99a fastalineno@Base 0.99a fastaout@Base 0.99a fastaparse@Base 0.99a fastapop_buffer_state@Base 0.99a fastapush_buffer_state@Base 0.99a fastarealloc@Base 0.99a fastarestart@Base 0.99a fastaset_debug@Base 0.99a fastaset_in@Base 0.99a fastaset_lineno@Base 0.99a fastaset_out@Base 0.99a fastatext@Base 0.99a fastay_check@Base 0.99a fastay_parse@Base 0.99a file_locate@Base 0.99a gcg_check@Base 0.99a gcg_crc@Base 0.99a gcg_create_buffer@Base 0.99a gcg_delete_buffer@Base 0.99a gcg_flex_debug@Base 0.99a gcg_flush_buffer@Base 0.99a gcg_parse@Base 0.99a gcg_print@Base 0.99a gcg_scan_buffer@Base 0.99a gcg_scan_bytes@Base 0.99a gcg_scan_string@Base 0.99a gcg_switch_to_buffer@Base 0.99a gcgalloc@Base 0.99a gcgfree@Base 0.99a gcgget_debug@Base 0.99a gcgget_in@Base 0.99a gcgget_leng@Base 0.99a gcgget_lineno@Base 0.99a gcgget_out@Base 0.99a gcgget_text@Base 0.99a gcgin@Base 0.99a gcgleng@Base 0.99a gcglex@Base 0.99a gcglex_destroy@Base 0.99a gcglineno@Base 0.99a gcgout@Base 0.99a gcgparse@Base 0.99a gcgpop_buffer_state@Base 0.99a gcgpush_buffer_state@Base 0.99a gcgrealloc@Base 0.99a gcgrestart@Base 0.99a gcgset_debug@Base 0.99a gcgset_in@Base 0.99a gcgset_lineno@Base 0.99a gcgset_out@Base 0.99a gcgtext@Base 0.99a gcgy_check@Base 0.99a gcgy_parse@Base 0.99a gde_check@Base 0.99a gde_create_buffer@Base 0.99a gde_delete_buffer@Base 0.99a gde_flex_debug@Base 0.99a gde_flush_buffer@Base 0.99a gde_parse@Base 0.99a gde_print@Base 0.99a gde_scan_buffer@Base 0.99a gde_scan_bytes@Base 0.99a gde_scan_string@Base 0.99a gde_switch_to_buffer@Base 0.99a gdealloc@Base 0.99a gdefree@Base 0.99a gdeget_debug@Base 0.99a gdeget_in@Base 0.99a gdeget_leng@Base 0.99a gdeget_lineno@Base 0.99a gdeget_out@Base 0.99a gdeget_text@Base 0.99a gdein@Base 0.99a gdeleng@Base 0.99a gdelex@Base 0.99a gdelex_destroy@Base 0.99a gdelineno@Base 0.99a gdeout@Base 0.99a gdeparse@Base 0.99a gdepop_buffer_state@Base 0.99a gdepush_buffer_state@Base 0.99a gderealloc@Base 0.99a gderestart@Base 0.99a gdeset_debug@Base 0.99a gdeset_in@Base 0.99a gdeset_lineno@Base 0.99a gdeset_out@Base 0.99a gdetext@Base 0.99a gdey_check@Base 0.99a gdey_parse@Base 0.99a genbank_check@Base 0.99a genbank_create_buffer@Base 0.99a genbank_delete_buffer@Base 0.99a genbank_flex_debug@Base 0.99a genbank_flush_buffer@Base 0.99a genbank_parse@Base 0.99a genbank_print@Base 0.99a genbank_scan_buffer@Base 0.99a genbank_scan_bytes@Base 0.99a genbank_scan_string@Base 0.99a genbank_switch_to_buffer@Base 0.99a genbankalloc@Base 0.99a genbankfree@Base 0.99a genbankget_debug@Base 0.99a genbankget_in@Base 0.99a genbankget_leng@Base 0.99a genbankget_lineno@Base 0.99a genbankget_out@Base 0.99a genbankget_text@Base 0.99a genbankin@Base 0.99a genbankleng@Base 0.99a genbanklex@Base 0.99a genbanklex_destroy@Base 0.99a genbanklineno@Base 0.99a genbankout@Base 0.99a genbankparse@Base 0.99a genbankpop_buffer_state@Base 0.99a genbankpush_buffer_state@Base 0.99a genbankrealloc@Base 0.99a genbankrestart@Base 0.99a genbankset_debug@Base 0.99a genbankset_in@Base 0.99a genbankset_lineno@Base 0.99a genbankset_out@Base 0.99a genbanktext@Base 0.99a genbanky_check@Base 0.99a genbanky_parse@Base 0.99a ig_check@Base 0.99a ig_create_buffer@Base 0.99a ig_delete_buffer@Base 0.99a ig_flex_debug@Base 0.99a ig_flush_buffer@Base 0.99a ig_parse@Base 0.99a ig_print@Base 0.99a ig_scan_buffer@Base 0.99a ig_scan_bytes@Base 0.99a ig_scan_string@Base 0.99a ig_switch_to_buffer@Base 0.99a igalloc@Base 0.99a igfree@Base 0.99a igget_debug@Base 0.99a igget_in@Base 0.99a igget_leng@Base 0.99a igget_lineno@Base 0.99a igget_out@Base 0.99a igget_text@Base 0.99a igin@Base 0.99a igleng@Base 0.99a iglex@Base 0.99a iglex_destroy@Base 0.99a iglineno@Base 0.99a igout@Base 0.99a igparse@Base 0.99a igpop_buffer_state@Base 0.99a igpush_buffer_state@Base 0.99a igrealloc@Base 0.99a igrestart@Base 0.99a igset_debug@Base 0.99a igset_in@Base 0.99a igset_lineno@Base 0.99a igset_out@Base 0.99a igtext@Base 0.99a igy_check@Base 0.99a igy_parse@Base 0.99a nbrf_check@Base 0.99a nbrf_create_buffer@Base 0.99a nbrf_delete_buffer@Base 0.99a nbrf_flex_debug@Base 0.99a nbrf_flush_buffer@Base 0.99a nbrf_parse@Base 0.99a nbrf_print@Base 0.99a nbrf_scan_buffer@Base 0.99a nbrf_scan_bytes@Base 0.99a nbrf_scan_string@Base 0.99a nbrf_switch_to_buffer@Base 0.99a nbrfalloc@Base 0.99a nbrffree@Base 0.99a nbrfget_debug@Base 0.99a nbrfget_in@Base 0.99a nbrfget_leng@Base 0.99a nbrfget_lineno@Base 0.99a nbrfget_out@Base 0.99a nbrfget_text@Base 0.99a nbrfin@Base 0.99a nbrfleng@Base 0.99a nbrflex@Base 0.99a nbrflex_destroy@Base 0.99a nbrflineno@Base 0.99a nbrfout@Base 0.99a nbrfparse@Base 0.99a nbrfpop_buffer_state@Base 0.99a nbrfpush_buffer_state@Base 0.99a nbrfrealloc@Base 0.99a nbrfrestart@Base 0.99a nbrfset_debug@Base 0.99a nbrfset_in@Base 0.99a nbrfset_lineno@Base 0.99a nbrfset_out@Base 0.99a nbrftext@Base 0.99a nbrfy_check@Base 0.99a nbrfy_parse@Base 0.99a parse_accadd@Base 0.99a parse_dscadd1@Base 0.99a parse_dscadd2@Base 0.99a parse_giadd@Base 0.99a parse_kwdadd@Base 0.99a parse_kwdupd@Base 0.99a parse_namadd@Base 0.99a parse_nuladd@Base 0.99a parse_stradd@Base 0.99a parse_veradd@Base 0.99a #MISSING: 0.99b+dfsg# pir_check@Base 0.99a #MISSING: 0.99b+dfsg# pir_checksum@Base 0.99a #MISSING: 0.99b+dfsg# pir_create_buffer@Base 0.99a #MISSING: 0.99b+dfsg# pir_delete_buffer@Base 0.99a #MISSING: 0.99b+dfsg# pir_flex_debug@Base 0.99a #MISSING: 0.99b+dfsg# pir_flush_buffer@Base 0.99a #MISSING: 0.99b+dfsg# pir_parse@Base 0.99a #MISSING: 0.99b+dfsg# pir_print@Base 0.99a #MISSING: 0.99b+dfsg# pir_scan_buffer@Base 0.99a #MISSING: 0.99b+dfsg# pir_scan_bytes@Base 0.99a #MISSING: 0.99b+dfsg# pir_scan_string@Base 0.99a #MISSING: 0.99b+dfsg# pir_switch_to_buffer@Base 0.99a #MISSING: 0.99b+dfsg# piralloc@Base 0.99a #MISSING: 0.99b+dfsg# pirfree@Base 0.99a #MISSING: 0.99b+dfsg# pirget_debug@Base 0.99a #MISSING: 0.99b+dfsg# pirget_in@Base 0.99a #MISSING: 0.99b+dfsg# pirget_leng@Base 0.99a #MISSING: 0.99b+dfsg# pirget_lineno@Base 0.99a #MISSING: 0.99b+dfsg# pirget_out@Base 0.99a #MISSING: 0.99b+dfsg# pirget_text@Base 0.99a #MISSING: 0.99b+dfsg# pirin@Base 0.99a #MISSING: 0.99b+dfsg# pirleng@Base 0.99a #MISSING: 0.99b+dfsg# pirlex@Base 0.99a #MISSING: 0.99b+dfsg# pirlex_destroy@Base 0.99a #MISSING: 0.99b+dfsg# pirlineno@Base 0.99a #MISSING: 0.99b+dfsg# pirout@Base 0.99a #MISSING: 0.99b+dfsg# pirparse@Base 0.99a #MISSING: 0.99b+dfsg# pirpop_buffer_state@Base 0.99a #MISSING: 0.99b+dfsg# pirpush_buffer_state@Base 0.99a #MISSING: 0.99b+dfsg# pirrealloc@Base 0.99a #MISSING: 0.99b+dfsg# pirrestart@Base 0.99a #MISSING: 0.99b+dfsg# pirset_debug@Base 0.99a #MISSING: 0.99b+dfsg# pirset_in@Base 0.99a #MISSING: 0.99b+dfsg# pirset_lineno@Base 0.99a #MISSING: 0.99b+dfsg# pirset_out@Base 0.99a #MISSING: 0.99b+dfsg# pirtext@Base 0.99a #MISSING: 0.99b+dfsg# piry_check@Base 0.99a #MISSING: 0.99b+dfsg# piry_parse@Base 0.99a protein_weight@Base 0.99a raw_check@Base 0.99a raw_create_buffer@Base 0.99a raw_delete_buffer@Base 0.99a raw_flex_debug@Base 0.99a raw_flush_buffer@Base 0.99a raw_parse@Base 0.99a raw_print@Base 0.99a raw_scan_buffer@Base 0.99a raw_scan_bytes@Base 0.99a raw_scan_string@Base 0.99a raw_switch_to_buffer@Base 0.99a rawalloc@Base 0.99a rawfree@Base 0.99a rawget_debug@Base 0.99a rawget_in@Base 0.99a rawget_leng@Base 0.99a rawget_lineno@Base 0.99a rawget_out@Base 0.99a rawget_text@Base 0.99a rawin@Base 0.99a rawleng@Base 0.99a rawlex@Base 0.99a rawlex_destroy@Base 0.99a rawlineno@Base 0.99a rawout@Base 0.99a rawparse@Base 0.99a rawpop_buffer_state@Base 0.99a rawpush_buffer_state@Base 0.99a rawrealloc@Base 0.99a rawrestart@Base 0.99a rawset_debug@Base 0.99a rawset_in@Base 0.99a rawset_lineno@Base 0.99a rawset_out@Base 0.99a rawtext@Base 0.99a rawy_check@Base 0.99a rawy_parse@Base 0.99a sequence_check@Base 0.99a sequence_fixnam@Base 0.99a sequence_format@Base 0.99a sequence_free@Base 0.99a sequence_new@Base 0.99a sequence_parse@Base 0.99a sequence_print@Base 0.99a sequence_strict@Base 0.99a sequence_type@Base 0.99a sprot_check@Base 0.99a sprot_create_buffer@Base 0.99a sprot_delete_buffer@Base 0.99a sprot_flex_debug@Base 0.99a sprot_flush_buffer@Base 0.99a sprot_parse@Base 0.99a sprot_print@Base 0.99a sprot_scan_buffer@Base 0.99a sprot_scan_bytes@Base 0.99a sprot_scan_string@Base 0.99a sprot_switch_to_buffer@Base 0.99a sprotalloc@Base 0.99a sprotfree@Base 0.99a sprotget_debug@Base 0.99a sprotget_in@Base 0.99a sprotget_leng@Base 0.99a sprotget_lineno@Base 0.99a sprotget_out@Base 0.99a sprotget_text@Base 0.99a sprotin@Base 0.99a sprotleng@Base 0.99a sprotlex@Base 0.99a sprotlex_destroy@Base 0.99a sprotlineno@Base 0.99a sprotout@Base 0.99a sprotparse@Base 0.99a sprotpop_buffer_state@Base 0.99a sprotpush_buffer_state@Base 0.99a sprotrealloc@Base 0.99a sprotrestart@Base 0.99a sprotset_debug@Base 0.99a sprotset_in@Base 0.99a sprotset_lineno@Base 0.99a sprotset_out@Base 0.99a sprottext@Base 0.99a sproty_check@Base 0.99a sproty_parse@Base 0.99a text_keyadd@Base 0.99a text_keyupd@Base 0.99a text_strupd@Base 0.99a text_strupds@Base 0.99a debian/libsquizz.lintian-overrides0000644000000000000000000000041712165743656014623 0ustar # Libraries do not worth specific packages (libsquizz-bioali0...). They # do the same job, only format is different. There is no use of a single # one besides the other. Both are packaged in "libsquizz" libsquizz: package-name-doesnt-match-sonames libbioali0 libbioseq0 debian/changelog0000644000000000000000000000302512263727166011054 0ustar squizz (0.99b+dfsg-3) unstable; urgency=low * Add auto-reconf build for ppc64el arch (Closes: #734828). Thanks to Logan Rosen -- Olivier Sallou Sat, 06 Jul 2013 09:46:23 +0200 squizz (0.99b+dfsg-2) unstable; urgency=low * Fix squizz dependency (Closes: #715120) -- Olivier Sallou Sat, 06 Jul 2013 09:35:43 +0200 squizz (0.99b+dfsg-1) unstable; urgency=low * New upstream release [ Anreas Tille ] * debian/copyright: - DEP5 - Add Files-Excluded to document what was removed from original source * debian/watch: handle +dfsg suffix -- Olivier Sallou Mon, 18 Feb 2013 11:55:27 +0200 squizz (0.99a-2) unstable; urgency=low [ Charles Plessy ] * Split debian/patches/debianpackaging into: debian/patches/correct-manpages-section.patch and debian/patches/disable-swissprot-test.patch for better readability. * Make the repacked upstream archive directory end in “.orig” (debian/get-orig-sources, see Developers Reference 3.4.4 §6.7.8.2). [ Andreas Tille ] * Section: libs (according to the decision of ftpmaster in override) * Standards-Version: 3.9.2 (no changes needed) * Debhelper 8 (control+compat) * Fixed Vcs fields * Enhanced short description Closes: #625929 -- Andreas Tille Thu, 05 Jan 2012 12:06:56 +0100 squizz (0.99a-1) unstable; urgency=low * Initial release (Closes: #618689) -- Olivier Sallou Fri, 18 Mar 2011 11:03:46 +0100 debian/squizz.install0000644000000000000000000000021312165743656012136 0ustar debian/tmp/usr/bin/squizz usr/bin/ debian/tmp/usr/share/man/man1/* usr/share/man/man1/ debian/tmp/usr/share/man/man5/* usr/share/man/man5/