[med-svn] [genometools] 03/03: new upstream release
Sascha Steinbiss
satta at debian.org
Fri Jul 22 11:13:21 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository genometools.
commit f73a143d3ee262baf7723a548e0ccb5537add406
Author: Sascha Steinbiss <satta at debian.org>
Date: Fri Jul 22 11:12:56 2016 +0000
new upstream release
---
debian/changelog | 7 +
debian/patches/adding_soname | 12 +-
debian/patches/gtdoc-traverse-sorted | 4 +-
debian/patches/ignore-m32-m64.patch | 2 +-
debian/patches/libbam-fix | 27 ++--
debian/patches/remove_png_timestamps | 12 +-
debian/patches/series | 2 -
debian/patches/spelling | 292 -----------------------------------
debian/patches/split-manuals | 14 +-
debian/patches/use-mx32 | 2 +-
debian/patches/use-pkgconfig | 191 -----------------------
11 files changed, 39 insertions(+), 526 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 6493cf0..4c32e4d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+genometools (1.5.9+ds-1) UNRELEASED; urgency=medium
+
+ * New upstream release.
+ * Update patches.
+
+ -- Sascha Steinbiss <satta at debian.org> Fri, 22 Jul 2016 10:50:40 +0000
+
genometools (1.5.8+ds-4) unstable; urgency=medium
* Make documentation builds reproducible.
diff --git a/debian/patches/adding_soname b/debian/patches/adding_soname
index 091e3e5..f0f8b89 100644
--- a/debian/patches/adding_soname
+++ b/debian/patches/adding_soname
@@ -13,10 +13,10 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
# compiled executables
GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
-@@ -618,8 +619,9 @@
- @echo "[link $(@F)]"
- @test -d $(@D) || mkdir -p $(@D)
- @$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
+@@ -621,8 +622,9 @@
+ $(V_ECHO) "[link $(@F)]"
+ $(V_DO)test -d $(@D) || mkdir -p $(@D)
+ $(V_DO)$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
- $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \
- -o $@ $(GTSHAREDLIB_LIBDEP)
+ $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
define PROGRAM_template
$(1): $(2)
-@@ -986,7 +988,8 @@
+@@ -989,7 +991,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
@@ -33,7 +33,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
+ cp lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib
+ ln -fs $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)$(SONAME_VERSION) $(prefix)/lib/libgenometools$(SHARED_OBJ_NAME_EXT)
endif
- @echo '[build config script $(@F)]'
+ $(V_ECHO) '[build config script $(@F)]'
sed -e 's!@CC@!$(CC)!' -e 's!@CFLAGS@!$(EXP_CFLAGS)!' \
--- a/gtpython/gt/dlload.py
+++ b/gtpython/gt/dlload.py
diff --git a/debian/patches/gtdoc-traverse-sorted b/debian/patches/gtdoc-traverse-sorted
index 4894f6c..1567e53 100644
--- a/debian/patches/gtdoc-traverse-sorted
+++ b/debian/patches/gtdoc-traverse-sorted
@@ -3,7 +3,7 @@ Description: gather API information by sorted traversal
Author: Sascha Steinbiss <satta at debian.org>
--- a/gtscripts/gtdoc.lua
+++ b/gtscripts/gtdoc.lua
-@@ -104,6 +104,25 @@
+@@ -118,6 +118,25 @@
end
end
@@ -29,7 +29,7 @@ Author: Sascha Steinbiss <satta at debian.org>
local export = nil
local is_lua = nil
-@@ -127,7 +146,7 @@
+@@ -141,7 +160,7 @@
for _, v in ipairs(export) do
local filename = gt_home .. "/" .. v
if is_dir(filename) then
diff --git a/debian/patches/ignore-m32-m64.patch b/debian/patches/ignore-m32-m64.patch
index 9dc274e..f781d65 100644
--- a/debian/patches/ignore-m32-m64.patch
+++ b/debian/patches/ignore-m32-m64.patch
@@ -2,7 +2,7 @@ Description: remove explicit -m32 and -m64
Author: Sascha Steinbiss <satta at debian.org>
--- a/Makefile
+++ b/Makefile
-@@ -360,22 +360,6 @@
+@@ -354,22 +354,6 @@
endif
endif
diff --git a/debian/patches/libbam-fix b/debian/patches/libbam-fix
index fb2b2b9..62b711a 100644
--- a/debian/patches/libbam-fix
+++ b/debian/patches/libbam-fix
@@ -5,17 +5,8 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
--- a/Makefile
+++ b/Makefile
-@@ -228,7 +228,7 @@
- # add necessary shared lib dependencies then not building them ourselves
- ifeq ($(useshared),yes)
- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-- -llua5.1-filesystem -llua5.1-des56 -lbam -ltre -lm -lpthread
-+ -llua5.1-filesystem -llua5.1-des56 -ltre -lm -lpthread
- else
- DEPLIBS:=
- endif
-@@ -597,6 +597,10 @@
- @$(RANLIB) $@
+@@ -600,6 +600,10 @@
+ $(V_DO)$(RANLIB) $@
endif
+ifeq ($(useshared),yes)
@@ -23,17 +14,17 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
+endif
+
lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
- @echo "[link $(@F)]"
- @test -d $(@D) || mkdir -p $(@D)
-@@ -615,13 +619,14 @@
+ $(V_ECHO) "[link $(@F)]"
+ $(V_DO)test -d $(@D) || mkdir -p $(@D)
+@@ -618,13 +622,14 @@
$(LIBGENOMETOOLS_OBJ) \
$(ADDITIONAL_SO_DEPS) \
$(ADDITIONAL_ZLIBS) \
+ $(ADDITIONAL_STATIC_DEPS) \
$(VERSION_SCRIPT)
- @echo "[link $(@F)]"
- @test -d $(@D) || mkdir -p $(@D)
- @$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
+ $(V_ECHO) "[link $(@F)]"
+ $(V_DO)test -d $(@D) || mkdir -p $(@D)
+ $(V_DO)$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
$(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \
-Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \
- -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
@@ -41,7 +32,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
define PROGRAM_template
$(1): $(2)
-@@ -634,46 +639,55 @@
+@@ -637,46 +642,55 @@
$(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
lib/libgenometools.a \
diff --git a/debian/patches/remove_png_timestamps b/debian/patches/remove_png_timestamps
index 6994d6c..57db40f 100644
--- a/debian/patches/remove_png_timestamps
+++ b/debian/patches/remove_png_timestamps
@@ -1,7 +1,7 @@
Description: Remove_png_timestamps
--- a/Makefile
+++ b/Makefile
-@@ -865,6 +865,10 @@
+@@ -910,6 +910,10 @@
bin/examples/sketch_constructed gtdata/sketch/default.style \
www/genometools.org/htdocs/images/constructed.png
endif
@@ -14,7 +14,7 @@ Description: Remove_png_timestamps
sed 'N;N;s/\n//' > /tmp/tmp.sed.$$$$ && \
--- a/doc/manuals/annotationsketch.tex
+++ b/doc/manuals/annotationsketch.tex
-@@ -240,7 +240,7 @@
+@@ -241,7 +241,7 @@
We will call the second part (after the ``\texttt{|}'') of these track titles \emph{track identifier strings} in the rest of this document.
\begin{figure}[ht]
@@ -23,7 +23,7 @@ Description: Remove_png_timestamps
\caption{Default AnnotationSketch output for a simple GFF3 file with simple \emph{exon}$\to$\emph{mRNA} collapsing.}
\label{tsexample1}
\end{figure}
-@@ -270,7 +270,7 @@
+@@ -271,7 +271,7 @@
Using this track selector function would produce the desired result of separate tracks for the \emph{mRNA} features for each strand (see Fig. \ref{tsexample2}).
\begin{figure}[ht]
@@ -32,7 +32,7 @@ Description: Remove_png_timestamps
\caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()} track selector function. This image now shows separate tracks for plus and minus strand features.}
\label{tsexample2}
\end{figure}
-@@ -312,7 +312,7 @@
+@@ -313,7 +313,7 @@
This code results in the image shown in Fig.~\ref{tsexample3} :
\begin{figure}[ht]
@@ -41,7 +41,7 @@ Description: Remove_png_timestamps
\caption{\AnnotationSketch output with \texttt{filter\_track\_selector()} track selector function. This image now shows a separate track for features with a specific caption.}
\label{tsexample3}
\end{figure}
-@@ -321,7 +321,7 @@
+@@ -322,7 +322,7 @@
There are kinds of data which may be interesting to see together with annotation renderings, but that can not be expressed -- or only in a complicated way -- in GFF3 format. It may even be too difficult or counterintuitive to properly represent this data as typical \AnnotationSketch box graphics. For example, this may be sequence data, numerical sequence analysis results, or other kinds of data which does not fit into the simple ‘genomic feature’ scheme. For an example, see Fig. \ref{ct [...]
\begin{figure}[ht]
@@ -50,7 +50,7 @@ Description: Remove_png_timestamps
\caption{Example \AnnotationSketch output with a custom track at the bottom, displaying the GC content over a window size of 200 bp.}
\label{ctexample1}
\end{figure}
-@@ -414,7 +414,7 @@
+@@ -415,7 +415,7 @@
Running layout and drawing functions on this diagram then produces the desired image (see Fig.~\ref{ctexample2}
\begin{figure}[ht]
diff --git a/debian/patches/series b/debian/patches/series
index 3fd76a2..abbaab0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-spelling
remove_png_timestamps
use-pkgconfig
adding_soname
@@ -8,5 +7,4 @@ fix-exports
split-manuals
use-mx32
gtdoc-traverse-sorted
-manual_fixed_dates.patch
ignore-m32-m64.patch
diff --git a/debian/patches/spelling b/debian/patches/spelling
index cd50c16..c89b308 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -3,295 +3,3 @@ Author: Sascha Steinbiss <satta at debian.org>
Forwarded: https://github.com/genometools/genometools/pull/727, https://github.com/genometools/genometools/pull/762, https://github.com/genometools/genometools/pull/767
Applied-Upstream: 1.5.9, commit:f47cc4a6e13d037d6342b0213a5739031ada59c1
Last-Update: 2016-03-15
---- a/gtdata/doc/fingerprint.lua
-+++ b/gtdata/doc/fingerprint.lua
-@@ -36,5 +36,5 @@
-
- - 0 everything went fine ('-check': the comparison was successful;
- '-duplicates': no duplicates found)
--- 1 an error occured ('-check': the comparison was not successful;
-+- 1 an error occurred ('-check': the comparison was not successful;
- '-duplicates': duplicates found)]])
---- a/src/core/error_api.h
-+++ b/src/core/error_api.h
-@@ -26,7 +26,7 @@
- This class is used for the handling of ___user errors___ in __GenomeTools__.
- Thereby, the actual <GtError> object is used to store the __error message__
- while it is signaled by the return value of the called function, if an error
-- occured.
-+ occurred.
-
- By convention in __GenomeTools__, the <GtError> object is always passed into
- a function as the last parameter and -1 (or <NULL> for constructors) is used
---- a/src/core/hashtable.h
-+++ b/src/core/hashtable.h
-@@ -81,14 +81,14 @@
- /**
- * @brief iterate over the hashtable in key order given by compare
- * function <cmp>
-- * @return 0 => no error, -1 => error occured
-+ * @return 0 => no error, -1 => error occurred
- */
- int gt_hashtable_foreach_ordered(GtHashtable *ht, Elemvisitfunc iter,
- void *data, GtCompare cmp,
- GtError *err);
- /**
- * @brief iterate over the hashtable in implementation-defined order
-- * @return 0 => no error, -1 => error occured
-+ * @return 0 => no error, -1 => error occurred
- */
- int gt_hashtable_foreach(GtHashtable *ht, Elemvisitfunc iter,
- void *data, GtError *err);
---- a/src/core/option_api.h
-+++ b/src/core/option_api.h
-@@ -34,14 +34,14 @@
-
- enum GtOPrval {
- GT_OPTION_PARSER_OK, /* Everything went fine. */
-- GT_OPTION_PARSER_ERROR, /* An error occured during option parsing. */
-+ GT_OPTION_PARSER_ERROR, /* An error occurred during option parsing. */
- GT_OPTION_PARSER_REQUESTS_EXIT /* The option parser requests an exit, because
- option -help, -help+, -helpdev, or -version
- was used. */
- };
-
- /* Possible option parser return values. <GT_OPTION_PARSER_OK> denotes that
-- everything went fine, <GT_OPTION_PARSER_ERROR> that an error occured during
-+ everything went fine, <GT_OPTION_PARSER_ERROR> that an error occurred during
- option parsing, and <GT_OPTION_PARSER_REQUESTS_EXIT> that the option parser
- requests an exit, because option <-help>, <-help+>, <-helpdev> or <-version>
- was used. */
---- a/src/core/seq_iterator_api.h
-+++ b/src/core/seq_iterator_api.h
-@@ -40,7 +40,7 @@
- /* Get next <sequence> (of length <len>) and <description> from <seqit>.
- Note that <seqit> retains ownership of the <sequence> and <description>.
- Returns 1 if another sequence could be parsed, 0 if all given sequence
-- files are exhausted, And -1 if an error occured (<err> is set
-+ files are exhausted, And -1 if an error occurred (<err> is set
- accordingly). */
- int gt_seq_iterator_next(GtSeqIterator *seqit,
- const GtUchar **sequence,
---- a/src/extended/node_stream_api.h
-+++ b/src/extended/node_stream_api.h
-@@ -35,7 +35,7 @@
- If no error occurs, 0 is returned and <genome_node> contains either the next
- <GtGenomeNode> or <NULL>, if the <node_stream> is exhausted.
- If an error occurs, -1 is returned and <err> is set accordingly (the status
-- of <genome_node> is undefined, but no ownership transfer occured). */
-+ of <genome_node> is undefined, but no ownership transfer occurred). */
- int gt_node_stream_next(GtNodeStream *node_stream,
- GtGenomeNode **genome_node,
- GtError *err);
---- a/src/gth/intermediate.c
-+++ b/src/gth/intermediate.c
-@@ -515,7 +515,7 @@
- if (XML_Parse(parser, gt_str_get(line), gt_str_length(line), false) ==
- XML_STATUS_ERROR) {
- error = XML_GetErrorCode(parser);
-- gt_error_set(err, "an error occured parsing line "GT_WU
-+ gt_error_set(err, "an error occurred parsing line "GT_WU
- " of file \"%s\": %s",
- parseinfo.linenumber, outputfilename,
- XML_ErrorString(error));
-@@ -530,7 +530,7 @@
- /* finish parsing */
- if (XML_Parse(parser, NULL, 0, true) == XML_STATUS_ERROR) {
- error = XML_GetErrorCode(parser);
-- gt_error_set(err, "an error occured while finishing the parsing of file "
-+ gt_error_set(err, "an error occurred while finishing the parsing of file "
- "\"%s\": %s", outputfilename, XML_ErrorString(error));
- had_err = -1;
- }
---- a/src/match/eis-encidxseq-construct.h
-+++ b/src/match/eis-encidxseq-construct.h
-@@ -118,7 +118,7 @@
- * suffix-array data structure to read construction from and progress
- * information
- * @param alphabet encoding to use for the built sequence, "ownership"
-- * of alphabet will pass to the returned object if no error occured.
-+ * of alphabet will pass to the returned object if no error occurred.
- * @param totalLen length of indexed sequence (including terminator
- * and separators)
- * @param projectName base name of corresponding suffixerator project
---- a/src/match/eis-encidxseq.h
-+++ b/src/match/eis-encidxseq.h
-@@ -50,7 +50,7 @@
- * pass information that is kept across individual calls
- * @param err genometools error object reference
- * @return number of bits actually written, or (BitOffset)-1 if an
-- * error occured
-+ * error occurred
- */
- typedef BitOffset (*bitInsertFunc)(BitString cwDest, BitOffset cwOffset,
- BitString varDest, BitOffset varOffset,
-@@ -436,7 +436,7 @@
- * @param pos position for which to print context
- * @param fp print diagnostics to this file pointer
- * @param hint use this structure for hinting
-- * @return 0 if an I/O error occured wrt fp
-+ * @return 0 if an I/O error occurred wrt fp
- */
- static inline int
- EISPrintDiagsForPos(const EISeq *seqIdx, GtUword pos, FILE *fp,
---- a/www/genometools.org/htdocs/libgenometools.html
-+++ b/www/genometools.org/htdocs/libgenometools.html
-@@ -3197,7 +3197,7 @@
- This class is used for the handling of <strong>user errors</strong> in <em>GenomeTools</em>.
- Thereby, the actual <code>GtError</code> object is used to store the <em>error message</em>
- while it is signaled by the return value of the called function, if an error
-- occured.</p><p> By convention in <em>GenomeTools</em>, the <code>GtError</code> object is always passed into
-+ occurred.</p><p> By convention in <em>GenomeTools</em>, the <code>GtError</code> object is always passed into
- a function as the last parameter and -1 (or <code>NULL</code> for constructors) is used
- as return value to indicate that an error occurred.
- Success is usually indicated by 0 as return value or via a non-<code>NULL</code> object
-@@ -5879,7 +5879,7 @@
- If no error occurs, 0 is returned and <code>genome_node</code> contains either the next
- <code>GtGenomeNode</code> or <code>NULL</code>, if the <code>node_stream</code> is exhausted.
- If an error occurs, -1 is returned and <code>err</code> is set accordingly (the status
-- of <code>genome_node</code> is undefined, but no ownership transfer occured).
-+ of <code>genome_node</code> is undefined, but no ownership transfer occurred).
- </p>
- <hr>
- <a name="gt_node_stream_pull"></a>
-@@ -7430,7 +7430,7 @@
- Get next <code>sequence</code> (of length <code>len</code>) and <code>description</code> from <code>seqit</code>.
- Note that <code>seqit</code> retains ownership of the <code>sequence</code> and <code>description</code>.
- Returns 1 if another sequence could be parsed, 0 if all given sequence
-- files are exhausted, And -1 if an error occured (<code>err</code> is set
-+ files are exhausted, And -1 if an error occurred (<code>err</code> is set
- accordingly).
- </p>
- <hr>
---- a/www/genometools.org/htdocs/tools/gt_fingerprint.html
-+++ b/www/genometools.org/htdocs/tools/gt_fingerprint.html
-@@ -176,7 +176,7 @@
- </li>
- <li>
- <p>
--1 an error occured (<em>-check</em>: the comparison was not successful;
-+1 an error occurred (<em>-check</em>: the comparison was not successful;
- <em>-duplicates</em>: duplicates found)
- </p>
- </li>
---- a/src/match/eis-encidxseq.c
-+++ b/src/match/eis-encidxseq.c
-@@ -50,7 +50,7 @@
- { \
- switch (retcode) { \
- case EIS_INTEGRITY_CHECK_INVALID_SYMBOL: \
-- fprintf(stderr, "Comparision failed at position "GT_WU"" \
-+ fprintf(stderr, "Comparison failed at position "GT_WU"" \
- ", reference symbol: %u, symbol read: %u\n", \
- pos, symOrig, symEnc); \
- gt_error_set(err, "Invalid symbol encountered."); \
---- a/src/tools/gt_compreads_decompress.c
-+++ b/src/tools/gt_compreads_decompress.c
-@@ -119,7 +119,7 @@
- gt_option_parser_add_option(op, option);
-
- option = gt_option_new_uword("width",
-- "set width of output, 0 disables formating. "
-+ "set width of output, 0 disables formatting. "
- "line breaks in quality strings can cause "
- "problems with parsers, use with care",
- &arguments->width, 0);
---- a/src/tools/gt_kmer_database.c
-+++ b/src/tools/gt_kmer_database.c
-@@ -109,7 +109,7 @@
- gt_option_imply(option_use_cutoff, option);
-
- /* -set_cutoff */
-- option = gt_option_new_uword_min("set_cutoff", "kmers occuring more often "
-+ option = gt_option_new_uword_min("set_cutoff", "kmers occurring more often "
- "than this value won't be saved",
- &arguments->cutoff_value, (GtUword) 30,
- (GtUword) 1);
---- a/gtdata/doc/extractseq.lua
-+++ b/gtdata/doc/extractseq.lua
-@@ -46,7 +46,7 @@
-
- If the end of the argument list only contains one filename, say fastaindex, then
- it is checked if there is a file `fastaindex.kys`. This makes up part of the
--fasta index, which is contructed by calling the suffixerator tool as follows:
-+fasta index, which is constructed by calling the suffixerator tool as follows:
-
- gt suffixerator -protein -ssp -tis -des -sds -kys -indexname fastaindex \
- -db inputfile1 [inputfile2 ..]
---- a/src/gth/parse_options.c
-+++ b/src/gth/parse_options.c
-@@ -381,7 +381,7 @@
- gt_option_parser_add_option(op, optverbose);
-
- /* -verboseseqs */
-- optverboseseqs = gt_option_new_bool("verboseseqs", "show additonal sequence "
-+ optverboseseqs = gt_option_new_bool("verboseseqs", "show additional sequence "
- "information\n(for debugging purposes)",
- &call_info->out->verboseseqs, false);
- gt_option_is_development_option(optverboseseqs);
---- a/www/genometools.org/htdocs/tools/gt_extractseq.html
-+++ b/www/genometools.org/htdocs/tools/gt_extractseq.html
-@@ -211,7 +211,7 @@
- </ul></div>
- <div class="paragraph"><p>If the end of the argument list only contains one filename, say fastaindex, then
- it is checked if there is a file <tt>fastaindex.kys</tt>. This makes up part of the
--fasta index, which is contructed by calling the suffixerator tool as follows:</p></div>
-+fasta index, which is constructed by calling the suffixerator tool as follows:</p></div>
- <div class="literalblock">
- <div class="content">
- <pre><tt>gt suffixerator -protein -ssp -tis -des -sds -kys -indexname fastaindex \
---- a/src/extended/affinealign.h
-+++ b/src/extended/affinealign.h
-@@ -52,7 +52,7 @@
-
- /* Computes a global alignment with affine gapcosts in square space. Use of this
- function requires an initialised <scorehandler> with cost values an
-- initalised <spacemanager>, the target alignment <align> and input sequences
-+ initialised <spacemanager>, the target alignment <align> and input sequences
- <useq> and <vseq> and lengths <ulen> and <vlen>. Returns affine cost
- value of global alignment. */
- GtWord gt_affinealign_with_Management(GtLinspaceManagement *spacemanager,
---- a/src/extended/type_node.c
-+++ b/src/extended/type_node.c
-@@ -109,7 +109,7 @@
-
- That is, if X is_a Y and Z part_of Y, then Z part_of X.
-
-- The method maintains a <node_stack> containing the inital <node> and all
-+ The method maintains a <node_stack> containing the initial <node> and all
- its 'is_a' children.
-
- Example from Sequence Ontology (we are looking at mRNA and exon, see
---- a/src/gth/align_protein.c
-+++ b/src/gth/align_protein.c
-@@ -188,7 +188,7 @@
- return retracenames[retrace];
- }
-
--/* the following function initalizes the input structure */
-+/* the following function initializes the input structure */
- static void initinput(GthAlignInputProtein *input,
- const unsigned char *ref_seq_orig,
- GthInput *gth_input)
---- a/src/tools/gt_condenseq_compress.c
-+++ b/src/tools/gt_condenseq_compress.c
-@@ -108,7 +108,7 @@
-
- /* -initsize */
- option = gt_option_new_uword("initsize",
-- "length of inital unique database in bases, "
-+ "length of initial unique database in bases, "
- "should be larger than -alignlength",
- &arguments->initsize, GT_UNDEF_UWORD);
- gt_option_parser_add_option(op, option);
---- a/src/tools/gt_linspace_align.c
-+++ b/src/tools/gt_linspace_align.c
-@@ -186,7 +186,7 @@
- optionshowscore = gt_option_new_bool("showscore", "show score for alignment, "
- "please note it will calculate costs "
- "for global alignments and scores for "
-- "local alignemnts always, independtly "
-+ "local alignments always, independently "
- "of input ",
- &arguments->showscore, false);
- gt_option_parser_add_option(op, optionshowscore);
diff --git a/debian/patches/split-manuals b/debian/patches/split-manuals
index efb1ae3..4585f12 100644
--- a/debian/patches/split-manuals
+++ b/debian/patches/split-manuals
@@ -206,7 +206,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
\author{\begin{tabular}{c}
\textit{Stefan Kurtz}\\
-@@ -64,7 +41,6 @@
+@@ -65,7 +42,6 @@
which specify to use a packed index or an enhanced suffix array for
a given set of subject sequences.
@@ -214,7 +214,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
\Program computes for all positions \(i\) in each unit, say \(s\) of length
\(n\), the length \(\Mup{i}\) of the minimum unique prefix
at position \(i\), if it exists. Uniqueness always refers to all substrings
-@@ -84,17 +60,6 @@
+@@ -85,17 +61,6 @@
substring. In this case, the program reports nothing for the corresponding
unit. The program was developed for designing whole genome tiling arrays.
The corresponding publication is \cite{GRAE:NIE:KUR:HUY:BIR:STU:FLI:2007}.
@@ -232,7 +232,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
The following options are available in \Program:
-@@ -121,7 +86,6 @@
+@@ -122,7 +87,6 @@
gzipped format, in which case they have to end with the suffix \texttt{.gz}.
}
@@ -240,7 +240,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
\Option{min}{$\ell$}{
Specify the minimum length $\ell$ of the minimum unique prefixes.
That is, for each unit \(s\) and each positions \(i\) in \(s\), the program
-@@ -141,34 +105,6 @@
+@@ -142,34 +106,6 @@
Using the keyword $\Showoptionkey{sequence}$ shows the sequence content
of the match.
}
@@ -275,7 +275,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
\Helpoption
-@@ -212,7 +148,6 @@
+@@ -213,7 +149,6 @@
This is used in the following call to the program \Program:
@@ -283,7 +283,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
\begin{Output}
gt uniquesub -output querypos -min 20 -max 30 -query queryfile.fna
-pck human-all
-@@ -248,27 +183,7 @@
+@@ -249,27 +184,7 @@
1013 21 gttttttttttttactttata
...
\end{Output}
@@ -311,7 +311,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
%\bibliographystyle{plain}
%\bibliography{defines,kurtz}
\begin{thebibliography}{1}
-@@ -280,5 +195,4 @@
+@@ -281,5 +196,4 @@
\newblock {\em {Bioinformatics}}, {23 ISMB/ECCB 2007}:{i195--i204}, 2007.
\end{thebibliography}
diff --git a/debian/patches/use-mx32 b/debian/patches/use-mx32
index 005b988..85b690c 100644
--- a/debian/patches/use-mx32
+++ b/debian/patches/use-mx32
@@ -1,7 +1,7 @@
Description: Use mx32
--- a/Makefile
+++ b/Makefile
-@@ -360,17 +360,19 @@
+@@ -354,17 +354,19 @@
endif
endif
diff --git a/debian/patches/use-pkgconfig b/debian/patches/use-pkgconfig
index 5a55300..42f0d21 100644
--- a/debian/patches/use-pkgconfig
+++ b/debian/patches/use-pkgconfig
@@ -9,186 +9,6 @@ Subject: [PATCH 1/6] Makefile: Drop spurious '$(3)'
Makefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
---- a/Makefile
-+++ b/Makefile
-@@ -16,17 +16,7 @@
- # OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
- #
-
--INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj \
-- -I$(CURDIR)/src/external/zlib-1.2.8 \
-- -I$(CURDIR)/src/external/md5-1.1.2/src \
-- -I$(CURDIR)/src/external/lua-5.1.5/src \
-- -I$(CURDIR)/src/external/luafilesystem-1.5.0/src \
-- -I$(CURDIR)/src/external/lpeg-0.10.2 \
-- -I$(CURDIR)/src/external/expat-2.0.1/lib \
-- -I$(CURDIR)/src/external/bzip2-1.0.6 \
-- -I$(CURDIR)/src/external/samtools-0.1.18 \
-- -I$(CURDIR)/src/external/sqlite-3.8.7.1 \
-- -I$(CURDIR)/src/external/tre/include/tre
-+INCLUDEOPT:=-I$(CURDIR)/src -I$(CURDIR)/obj
-
- ifeq ($(shell pkg-config --version > /dev/null 2> /dev/null; echo $$?),0)
- HAS_PKGCONFIG:=yes
-@@ -37,6 +27,48 @@
- HAS_PKGCONFIG:=no
- endif
-
-+# add necessary shared lib dependencies instead of building them ourselves
-+ifeq ($(useshared),yes)
-+ ifeq ($(HAS_PKGCONFIG),yes)
-+ DEPLIBS:=-lbz2 \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs zlib) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs expat) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua-5.1) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-lpeg) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-md5) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-filesystem) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs lua5.1-des56) \
-+ -lbam \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --libs tre) \
-+ -lm -lpthread
-+ INCLUDEOPT+=$(shell $(OVERRIDE_PC_PATH) pkg-config --cflags zlib) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags expat) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua-5.1) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-lpeg) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-md5) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-filesystem) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags lua5.1-des56) \
-+ $(shell $(OVERRIDE_PC_PATH) pkg-config --cflags tre)
-+ else
-+ # Requested the use of shared libraries without having pkg-config.
-+ # You are on your own. Good luck.
-+ DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
-+ -llua5.1-filesystem -llua5.1-des56 -lbam -ltre -lm -lpthread
-+ endif
-+else
-+ DEPLIBS:=
-+ INCLUDEOPT+=-I$(CURDIR)/src/external/zlib-1.2.8 \
-+ -I$(CURDIR)/src/external/md5-1.1.2/src \
-+ -I$(CURDIR)/src/external/lua-5.1.5/src \
-+ -I$(CURDIR)/src/external/luafilesystem-1.5.0/src \
-+ -I$(CURDIR)/src/external/lpeg-0.10.2 \
-+ -I$(CURDIR)/src/external/expat-2.0.1/lib \
-+ -I$(CURDIR)/src/external/bzip2-1.0.6 \
-+ -I$(CURDIR)/src/external/samtools-0.1.18 \
-+ -I$(CURDIR)/src/external/sqlite-3.8.7.1 \
-+ -I$(CURDIR)/src/external/tre/include
-+endif
-+
- ifneq ($(cairo),no)
- # XXX: check for existence of packages, and emit warning and disable cairo
- # if packages are not available
-@@ -125,6 +157,7 @@
- LIBEXPAT_DEP:=$(LIBEXPAT_SRC:%.c=obj/%.d)
-
- TRE_DIR:=src/external/tre/lib
-+TRE_CPPFLAGS=-I$(CURDIR)/src/external/tre/include/tre
- LIBTRE_SRC:=$(TRE_DIR)/regcomp.c $(TRE_DIR)/regerror.c $(TRE_DIR)/regexec.c \
- $(TRE_DIR)/tre-ast.c $(TRE_DIR)/tre-compile.c \
- $(TRE_DIR)/tre-filter.c $(TRE_DIR)/tre-match-backtrack.c \
-@@ -743,6 +776,15 @@
- @$(CC) -c $< -o $(@:.o=.d) -DHAVE_MALLOC_USABLE_SIZE $(EXP_CPPFLAGS) \
- $(GT_CPPFLAGS) $(3) -MM -MP -MT $@ $(FPIC)
-
-+# TRE needs special attention
-+obj/$(TRE_DIR)/%.o: $(TRE_DIR)/%.c
-+ $(V_ECHO) "[compile $(@F)]"
-+ $(V_DO)test -d $(@D) || mkdir -p $(@D)
-+ $(V_DO)$(CC) -c $< -o $@ $(EXP_CPPFLAGS) \
-+ $(GT_CPPFLAGS) $(EXP_CFLAGS) $(TRE_CPPFLAGS) $(FPIC)
-+ $(V_DO)$(CC) -c $< -o $(@:.o=.d) $(EXP_CPPFLAGS) \
-+ $(GT_CPPFLAGS) $(TRE_CPPFLAGS) -MM -MP -MT $@ $(FPIC)
-+
- define COMPILE_template
- $(1): $(2)
- @echo "[compile $$(@F)]"
-@@ -1001,10 +1043,10 @@
- src_check src/ltr/*
-
- splintclean:
-- find obj -name '*.splint' | xargs rm -f
-+ find obj -name '*.splint' -delete
-
- sbclean:
-- find obj -name '*.sb' | xargs rm -f
-+ find obj -name '*.sb' -delete
-
- obj/%.sb: src/match/%.c
- @echo "scan-build $<"
-@@ -1070,7 +1112,7 @@
- headercheck:${ALLHEADER}
-
- headerclean:
-- find obj -name '*.check' | xargs rm -f
-+ find obj -name '*.check' -delete
-
- obj/%.check: ${CURDIR}/src/match/%.h
- @echo "check include $<"
-@@ -1139,7 +1181,7 @@
-
- clean:
- rm -rf lib
-- find obj -name '*.o' |xargs rm -f
-+ find obj -name '*.o' -delete
- rm -f obj/amalgamation.c
- rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests
- $(MAKE) -s -C $(CURDIR)/doc/devguide clean
---- a/src/core/grep.c
-+++ b/src/core/grep.c
-@@ -23,7 +23,7 @@
- #include "core/ma.h"
- #include "core/str.h"
- #include "core/unused_api.h"
--#include "tre.h"
-+#include <tre/tre.h>
-
- static void grep_error(int errcode, regex_t *matcher, GtError *err)
- {
---- a/src/extended/rcr.c
-+++ b/src/extended/rcr.c
-@@ -48,7 +48,7 @@
- #include "extended/sam_alignment.h"
- #include "extended/sam_query_name_iterator.h"
- #include "extended/samfile_iterator.h"
--#include "sam.h"
-+#include <samtools/sam.h>
-
- #define BAMBASEA 1
- #define BAMBASEC 2
---- a/src/extended/sam_alignment.c
-+++ b/src/extended/sam_alignment.c
-@@ -16,7 +16,7 @@
- OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
- */
-
--#include <sam.h>
-+#include <samtools/sam.h>
- #include "core/alphabet_api.h"
- #include "core/ensure.h"
- #include "core/ma_api.h"
---- a/src/extended/sam_alignment_rep.h
-+++ b/src/extended/sam_alignment_rep.h
-@@ -23,7 +23,7 @@
- /* The contents of this file is to be considered private implementation detail.
- */
-
--#include <sam.h>
-+#include <samtools/sam.h>
- #include "core/alphabet_api.h"
-
- struct GtSamAlignment{
---- a/src/extended/samfile_iterator.c
-+++ b/src/extended/samfile_iterator.c
-@@ -15,7 +15,7 @@
- OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
- */
-
--#include <sam.h>
-+#include <samtools/sam.h>
- #include "core/cstr_api.h"
- #include "core/ensure.h"
- #include "core/error_api.h"
--- /dev/null
+++ b/src/external/lpeg-0.10.2/lua-lpeg.h
@@ -0,0 +1,39 @@
@@ -231,14 +51,3 @@ Subject: [PATCH 1/6] Makefile: Drop spurious '$(3)'
+ size_t l); /* size of data to be passed to 'f' */
+
+#endif
---- a/src/gtr.c
-+++ b/src/gtr.c
-@@ -24,7 +24,7 @@
- #include "lauxlib.h"
- #include "lualib.h"
- #include "lfs.h"
--#include "lpeg.h"
-+#include "lua-lpeg.h"
- #include "md5.h"
- #include "ldes56.h"
- #include "core/compat.h"
--
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