[med-svn] [andi] 01/08: Imported Upstream version 0.9.4.1
Fabian Klötzl
kloetzl-guest at moszumanska.debian.org
Wed Oct 7 09:04:08 UTC 2015
This is an automated email from the git hooks/post-receive script.
kloetzl-guest pushed a commit to branch master
in repository andi.
commit def050e2d52aaf664bd6be016b236e37a925b10a
Author: Fabian Klötzl <fabian at kloetzl.info>
Date: Wed Oct 7 10:42:55 2015 +0200
Imported Upstream version 0.9.4.1
---
.gitignore | 79 +
.travis.yml | 37 +
ChangeLog | 3583 -------------------
Makefile.in | 1208 -------
README | 66 -
aclocal.m4 | 1370 --------
ar-lib | 270 --
compile | 347 --
configure | 7968 -------------------------------------------
configure.ac | 4 +-
depcomp | 791 -----
docs/Makefile.in | 505 ---
docs/andi.1 | 56 -
docs/manual/andi-manual.tex | 386 +++
docs/manual/andi_labels.pdf | Bin 0 -> 2833 bytes
docs/manual/references.bib | 112 +
docs/manual/version.tex.in | 2 +
install-sh | 527 ---
libs/Makefile.in | 549 ---
missing | 215 --
opt/Makefile.in | 536 ---
opt/psufsort/Makefile.in | 577 ----
scripts/maf2phy.awk | 59 +
scripts/vmatch.sh | 26 +
src/Makefile.in | 724 ----
src/config.hin | 146 -
test-driver | 139 -
test/Makefile.in | 686 ----
28 files changed, 703 insertions(+), 20265 deletions(-)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..221fdf5
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,79 @@
+# Binary and automatically generated files
+*.o
+*.a
+andi
+andi_*
+randomSeed.dat
+seedms
+testRMQ
+src/config.h
+src/stamp-h1
+src/config.hin
+src/config.hin~
+
+#docs
+docs/doxygen_sqlite3.db
+docs/html/*
+docs/latex/*
+docs/andi.1
+*.aux
+*.auxlock
+*.dep
+*.dpth
+*.toc
+*.out
+*.pdf
+*.backup
+*.bbl
+*.blg
+!andi-manual.pdf
+
+*.in
+!docs/andi.1.in
+!docs/manual/version.tex.in
+docs/manual/version.tex
+*.log
+**/Makefile
+configure.scan
+config.status
+depcomp
+install-sh
+aclocal.m4
+**/.deps/
+autom4te.cache/
+README
+ChangeLog
+missing
+compile
+configure
+ar-lib
+src/.dirstamp
+
+# test files
+*.fasta
+cachegrind*
+callgrind*
+test.trs
+test-driver
+test_esa
+test_seq
+test_fasta
+*.trs
+
+# Coverage
+*.gcda
+*.gcno
+*.gcov
+
+
+andi.sublime-*
+
+# for legacy git only:
+libs/RMQ/.deps/
+libs/RMQ/Makefile
+Makefile
+
+# Profiling:
+gmon.out
+profile
+
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..bc97df0
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1,37 @@
+language: cpp
+compiler:
+- gcc
+before_install:
+- sudo pip install cpp-coveralls
+- sudo add-apt-repository ppa:ubuntu-toolchain-r/test -y
+- sudo apt-get update -qq
+- if [ "$CXX" = "g++" ]; then sudo apt-get install -qq g++-4.8; fi
+- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
+- sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90
+- sudo apt-get install libglib2.0-dev
+- wget https://libdivsufsort.googlecode.com/files/libdivsufsort-2.0.1.tar.gz
+- tar -xzvf libdivsufsort-2.0.1.tar.gz
+- cd libdivsufsort-2.0.1
+- mkdir build
+- cd build
+- cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="/usr/local" ..
+- make
+- sudo make install
+- cd $TRAVIS_BUILD_DIR
+- export LD_LIBRARY_PATH=/usr/local:$LD_LIBRARY_PATH
+script:
+- export LD_LIBRARY_PATH=/usr/local/lib:/usr/local:$LD_LIBRARY_PATH
+- export OMP_NUM_THREADS=4
+- autoreconf -fvi -Im4
+- ./configure --enable-unit-tests CFLAGS='-fprofile-arcs -ftest-coverage' CXXFLAGS='-fprofile-arcs -ftest-coverage'
+- make
+- make check
+- make distcheck
+- tar xzvf andi-*.tar.gz
+- cd andi-*
+- ./configure --enable-unit-tests --without-libdivsufsort
+- make
+- make check
+- cd ..
+after_success:
+- coveralls --exclude libdivsufsort-2.0.1 --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'
diff --git a/ChangeLog b/ChangeLog
deleted file mode 100644
index fc37a5c..0000000
--- a/ChangeLog
+++ /dev/null
@@ -1,3583 +0,0 @@
-commit 357a1f1
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-25
-
- release v0.9.4
-
-commit 44d8361
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- delete temporary files
-
-commit eab44f8
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- test low-memory mode
-
-commit bb44d77
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- silence tests
-
-commit f0066b7
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- adds extra tests
-
-commit f621895
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- checks if andi can be executed
-
-commit a2e4bfc
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- fixes issue with more than three sequences
-
-commit 3136215
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- ignore weird config header
-
-commit f7fa17a
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- removes AC_FUNC_{M,RE}ALLOC checks
-
-commit 5db1332
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- adds manual to top directory
-
-commit 8b41ccd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- changes manual paths
-
-commit a6a5a31
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-19
-
- improves manual building
-
-commit 7b02992
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- Doxyfile is not a pdf
-
-commit 563683e
-Merge: 3c22106 0eaead6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- Merge branch 'master' into manual
-
- Conflicts:
- Makefile.am
- docs/manual/andi-manual.pdf
-
-commit 0eaead6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- updates known issues
-
-commit cec0f13
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- uses reallocarray for arrays
-
-commit d9353a3
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- mention other licenses
-
-commit 60a3f4d
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- fix coverage
-
-commit dfc24d6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- test dist and psufsort via travis CI
-
-commit 76708ef
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- list subdirs explicitly to avoid dist errors
-
-commit 3665e3b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- adds interface.h to source files
-
-commit d236756
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- improves makefiles
-
-commit cb1281e
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- improves build system
-
-commit 7f8f3fa
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- the tests require a working andi
-
-commit c77aa39
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- fixes andi build
-
-commit 6a1eaef
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- adds files for compat lib
-
-commit 37fbf22
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- removes config.hin from version control
-
-commit 8f59a90
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-18
-
- adds compatibility library
-
-commit f3f51a9
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-17
-
- adds configure checks
-
-commit 9bd8c3f
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-09-17
-
- replaces kseq with pfasta
-
- Switched to pfasta, the pedantic FASTA parsing library. See
- https://github.com/kloetzl/pfasta for details.
-
-commit 3c22106
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-31
-
- fix versioning in manual
-
-commit 47c3c95
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-31
-
- fixes typo
-
-commit a7f3dd3
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-31
-
- adds version number into manual
-
-commit 354defb
-Merge: 4adb3df 79d8155
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-31
-
- Merge branch 'master' into manual
-
-commit 79d8155
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-31
-
- bumps version number
-
-commit c43d478
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-31
-
- release v0.9.3
-
-commit c8b3c7f
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-03
-
- improves asymmetric distance handling
-
- The anchor distance is not symmetric. i.e. d(i,j) != d(j,i). Thus
- we computed both distances and average the result. Now, when computing
- the average, the individual distances are weighted by the coverage.
-
-commit 4c60dfd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-07-03
-
- improves distance matrix handling
-
-commit 1df25aa
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-26
-
- improves man page
-
-commit f4f44dd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-26
-
- improve synopsis
-
-commit 4adb3df
-Merge: 0b0a06b 80516e8
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-26
-
- Merge branch 'master' into manual
-
-commit 80516e8
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-26
-
- test for relative error
-
-commit 686376d
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-26
-
- count long anchors as homologous
-
- Sometimes a single long anchor spans a whole contig. Then no second anchors,
- neither left nor right, can be found. In this case, count the long anchor
- as homologous if its length is double the threshold.
-
-commit 2d7df3c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-25
-
- use proper NAN
-
-commit 0b0a06b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-16
-
- adds comments
-
-commit 005b7bf
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-16
-
- copy manual to the top dir
-
-commit b144e6e
-Merge: 14b4cf0 0b90106
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-09
-
- Merge branch 'esa_opt'
-
-commit 14b4cf0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-09
-
- bumps version number
-
-commit efe4a9d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-09
-
- release v0.9.2
-
-commit 0b90106
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-04
-
- Revert "merges FVC and LCP"
-
- This reverts commit 632b069da544f9f54f96985ba03b627e20c0c2c2, because that
- commit imposes a maximum LCP limit at 2^24. This could be problematic for
- big mammalian genomes. Also the runtime improvement of this feature was
- smaller than expected.
-
- Conflicts:
- src/esa.c
-
-commit 18156ac
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-04
-
- adds constness
-
-commit 6667295
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-04
-
- adds fallback for strchrnul
-
- Apparently, `strchrnul(3)` is a GNU specific function and unavailable on
- BSD and Darwin (OS X). Thus we have to check for its existance and
- provide a fallback function. Thanks to Marc Garcia-Garcera for pointing
- this out.
-
-commit 0ee3413
-Merge: a66c812 707fd3f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-02
-
- Merge branch 'master' into esa_opt
-
- Conflicts:
- src/esa.c
-
-commit 707fd3f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-02
-
- bumps version number
-
-commit ce94f7b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-02
-
- release v0.9.1
-
-commit db86b56
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-02
-
- Adds reference to blog post by @katholt to manual
-
-commit 9b5308d
-Merge: 26fe4a9 a72c573
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-02
-
- Merge branch 'master' of github.com:EvolBioInf/andi
-
-commit 26fe4a9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-06-02
-
- solves issue where the manual would be overwritten
-
-commit a72c573
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-06-01
-
- display proper error during configuration when libdivsufsort is missing.
-
- fixes issue #3.
-
-commit 65b175d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-13
-
- ignore failing build with missing pdflatex
-
-commit 1857a7b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-13
-
- adds coverage badge
-
-commit 01906aa
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-08
-
- improves code-docs
-
-commit a66c812
-Merge: ced0c8d 74b5be9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-08
-
- Merge branch 'master' into esa_opt
-
-commit 74b5be9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-08
-
- improves readme
-
- - minor changes
- - adds dependency section as suggested by crashfrog in issue #2
-
-commit b803e4e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-08
-
- only build the manual when pdflatex is present
-
-commit 360451e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-05-08
-
- improves readme
-
-commit 2ce6e0d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- adds long form --threads argument
-
-commit e077cfb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- improves andi version string
-
-commit 3fde435
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- improves readme
-
-commit 41fe18a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- fixes andi reference
-
-commit 7178096
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- ignores more files
-
-commit b1189e2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- adds bibliography
-
-commit 8c84d23
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-30
-
- simplifies manual
-
- Delete the chapter copied from my thesis. If anyone is really interested in that, they should simply read the thesis.
-
-commit f8fb5a4
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-28
-
- ingore tex build files
-
-commit ea0fe1b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-28
-
- Adds Manual
-
- This commit adds the user manual for andi. It is written in LaTeX
- and thus compiles to PDF. Some images, which are not generated via
- LaTeX them selves, are given as .pdf. Further more .tex and .data
- files are given for advanced plots.
-
- Even though, one should not include generated files into source
- control, I include andi-manual.pdf. This way, I can link to it online.
- Also, a the user might not have LaTeX or the neccessary packages, to
- build the manual. Thus, the final result, but not intermediate steps,
- are committed.
-
-commit ced0c8d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-16
-
- check for too long input sequences
-
-commit ff99ceb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- more pass by value
-
-commit 14a500f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- pass intervals by value
-
-commit 3bb40ba
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- Revert "ensure matches are increasing"
-
- Sorry, for being stupid.
-
- This reverts commit 596771cb77ec197e04e9c91fc90f530f9c976ad3.
-
-commit 596771c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- ensure matches are increasing
-
-commit d0e6d93
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- adds address sanitizer make target
-
-commit fdd3b4e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- improves esa unit tests
-
-commit 67615be
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-15
-
- removes legacy typedef
-
-commit 3d9b402
-Merge: 420bf0a 8940c9d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-14
-
- Merge branch 'master' into esa_opt
-
-commit 8940c9d
-Merge: 7980acf ddd3996
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-14
-
- Merge branch 'master' of github.com:EvolBioInf/andi
-
-commit ddd3996
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-14
-
- adds contact details to readme
-
-commit 7980acf
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-14
-
- improves unit tests
-
-commit c9c7b6b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-12
-
- improves readme
-
-commit 420bf0a
-Merge: 5403ae9 c0df08d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- Merge branch 'master' into esa_opt
-
-commit c0df08d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- use a single thread for the unit tests
-
-commit 1279915
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- warn about -t in single threaded builds
-
-commit 5403ae9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- improves locality
-
-commit b69b074
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- avoids needless recomparison
-
-commit d6fcbcc
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- improves constness
-
-commit 089bfdb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- null freed pointers
-
-commit 422b66c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-10
-
- check for LCP overflow
-
-commit 632b069
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- merges FVC and LCP
-
-commit 4c225da
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- reduces memory usage
-
-commit d1b0438
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- renames esa_t to esa_s
-
-commit 4a91d27
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- updates help
-
-commit 8a140e0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- fixes bug introduced in 72b59da6
-
-commit d5b8dc7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- limits number of threads for travis builds
-
-commit 72b59da
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- simplifies code
-
-commit 526b891
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- just testing
-
-commit 7801887
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-09
-
- changes C standard to C99
-
-commit 4a842e0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- bumps version number
-
-commit 542b490
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- release v0.9
-
- This is version 0.9 of the `andi` tool for efficient estimation of evolutionary distances. It is faster and uses less memory than the last version. It also features a new suffix array construction algorithm: psufsort. That one can be activated via:
-
- ./configure --without-libdivsufsort
-
- Also, a lot of the code has been refactored to plain C. This reduces the dependencies and makes the code easier to maintain.
-
-commit 61d1379
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- fixes distribution issues
-
-commit 3c5fc09
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- fixes false flag
-
-commit 18580fb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- improves man page
-
-commit a7abb0f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- fixes readme
-
-commit 7aef3f6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-04-07
-
- use all processors by default
-
-commit e18b71a
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- adds newline
-
-commit edea232
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- fixes printf formatting for size_t
-
-commit b20d875
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- more simplifications
-
-commit 0fdb6d9
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- simplifies some code
-
-commit e924757
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- removes debug information
-
-commit 4b7a139
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- fixes use after free
-
-commit 90b17a0
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-04
-
- further improves join test case
-
-commit 0ec5de9
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-03
-
- improves join test case
-
-commit 82a4e5b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-03
-
- streamline more code
-
-commit 569924e
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-03
-
- adds static scoping
-
-commit 8d4e8dd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-03
-
- improves code
-
-commit e6922b8
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-03
-
- more simplifications
-
-commit 67df1fc
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-03
-
- Simplifies code
-
-commit c117cf6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- Revert "fixes tests"
-
- This reverts commit f9bb1730fc27670210a4c2fc4febc2ab07d64186.
- Removes now useless tests.
-
-commit 398a2b4
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- renames various functions
-
-commit f4cd87c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- renames get_interval_FVC to get_interval
-
-commit 02890ca
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- simplifies code
-
-commit df0e446
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- goto considered useful
-
-commit c2e53c3
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- Revert "fixes travis language"
-
- This reverts commit ef9a9b084964d0eca2d87362054dd9184782c9bb.
-
-commit 30e2046
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- moves function definitions
-
-commit ef9a9b0
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- fixes travis language
-
-commit 1cdcb61
-Merge: cbd5013 95ddbbf
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- Merge branch 'master' into travis
-
- Conflicts:
- .travis.yml
- configure.ac
-
-commit cbd5013
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- I dont know what I am doing wrong here
-
-commit 95ddbbf
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- fixes broken travis build, hopefully
-
-commit 11eac26
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- fixes feature test macro
-
-commit 4832109
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- fixes broken build
-
-commit bf5245e
-Merge: e91faab 5cb414e
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- Merge branch 'master' into travis
-
- Conflicts:
- .travis.yml
-
-commit 5cb414e
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- fixes broken coverage
-
-commit 04b0894
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-04-02
-
- removes old merge conflict
-
-commit 441f837
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-30
-
- fixes dejavu bug
-
-commit ca9c572
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-28
-
- removes useless instruction
-
-commit 687b35c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-28
-
- fixes C++ build weirdness
-
-commit a6a46fd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-28
-
- ignores stamp files
-
-commit 8bc60b4
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-28
-
- fixes c++ definition macro
-
-commit 993a668
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-28
-
- fixes compiler warnings
-
-commit 22fa316
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-28
-
- removes last traces of C++ in andi
-
-commit 305e7bc
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-27
-
- follow up fix
-
-commit 653e6f7
-Merge: 26f6556 2034a8c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-27
-
- Merge branch 'master' of https://github.com/kloetzl/andi
-
- Conflicts:
- src/Makefile.am
-
-commit 26f6556
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-03-26
-
- refactors all the code to plain C
-
- As the RMQs were the only dependency using C++, and we got rid of those,
- I refactored the code to plain C11. Thus we no longer need a C++ compiler,
- except for the unit tests, or psufsort. This might make andi easier to port
- to old machines without decent C++ compilers. Additionally, this now allows
- us to use the cool C features, missing in C++.
-
-commit 2034a8c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-03-25
-
- fixes perf make target
-
-commit 8148f7f
-Merge: 3505106 0c98b73
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-03-23
-
- Merge branch 'psufsort'
-
- Conflicts:
- Makefile.am
- src/esa.h
- test/Makefile.am
-
-commit 3505106
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-03-23
-
- bumps version number to 0.9-beta
-
-commit 336216a
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-22
-
- fixes everything
-
-commit f9bb173
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-22
-
- fixes tests
-
-commit dcab084
-Merge: bd7de82 cec5fd2
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-22
-
- Merge branch 'master' into no-rmq
-
- Conflicts:
- Makefile.am
- src/Makefile.am
- src/andi.cpp
- src/esa.cpp
- src/esa.h
- src/process.cpp
- test/Makefile.am
-
-commit cec5fd2
-Merge: 249fae4 b70f1d6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-02-19
-
- Merge branch 'master' of github.com:EvolBioInf/andi
-
-commit b70f1d6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-18
-
- if extra verbose, print asymmetric distances
-
-commit 249fae4
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-02-16
-
- adds flags for old versions of automake
-
-commit 0c98b73
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-11
-
- enables concurrency in psufsort
-
-commit 0cbd62f
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-11
-
- updates config.h template
-
-commit cdc676f
-Merge: a9c581c ed853dc
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-09
-
- Merge branch 'master' into psufsort
-
-commit ed853dc
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- fixes travis build
-
-commit e91faab
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- even more fixing
-
-commit 6f6fb76
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- may be
-
-commit 3d41793
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- further tests
-
-commit 6a23b73
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- adds some flags
-
-commit 90910fb
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- testing
-
-commit 747e78a
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- adds two more autoconf func checks
-
-commit a9c581c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- use autoconf C++11 macro
-
-commit 97b396d
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- follow up
-
-commit 5256361
-Merge: 80b83b0 a7df689
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- Merge branch 'master' into psufsort
-
-commit a7df689
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- improves readme
-
-commit 9363851
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- adds m4 macro for C++11 support
-
-commit e605395
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- removes unnecessary compile flags
-
-commit 780e5f4
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-08
-
- adds missing include
-
-commit 01212e9
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-07
-
- fixes invalid memory access in unit test
-
-commit 4ba4fb0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-02-05
-
- fixes maf2phy output format
-
-commit 80b83b0
-Merge: 5d1cdf5 73d16c1
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-04
-
- Merge branch 'master' into psufsort
-
- Conflicts:
- Makefile.am
-
-commit 73d16c1
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-04
-
- bumps version
-
-commit 7f7aca2
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-04
-
- release v0.8.1
-
-commit 735d4ee
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-04
-
- also distribute test scripts
-
-commit a2a1ee6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-04
-
- build a distribution with enabled unit tests
-
-commit 5d1cdf5
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-04
-
- adds psufsort
-
- Instead of libdivsufsort the suffix array can now be built with psufsort.
- The switch is made at configuration time.
-
-commit 858d871
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-03
-
- warn about too short sequences
-
-commit 56ea554
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-03
-
- improves warning for broken sequences
-
-commit 008efb6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-01
-
- removes gmon from make target
-
-commit d38c242
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-02-01
-
- improves docs
-
- - adds documentation for dist_hack
- - ignores doxygen sqlite file
-
-commit d0a5b4f
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-25
-
- fixes join test, again
-
-commit 0c3afc6
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-25
-
- fixes join test
-
-commit 6473063
-Merge: 39adc6c c3874bd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-25
-
- Merge branch 'master' into coverage
-
-commit c3874bd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-25
-
- adds test for join mode
-
-commit 39adc6c
-Merge: 8a22def bb8580b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-25
-
- Merge branch 'master' into coverage
-
-commit bb8580b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-25
-
- adds docs
-
-commit 4fe6be2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-01-09
-
- adds 'off' diagnostic
-
-commit 8f31a57
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-01-09
-
- improves diagnotics
-
-commit c6e8b6d
-Merge: 4b334be aa7296a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2015-01-08
-
- Merge branch 'master' of github.com:EvolBioInf/andi
-
-commit aa7296a
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2015-01-02
-
- bumps version number
-
-commit 69b2cef
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-25
-
- updates readme
-
-commit 4b334be
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-19
-
- bumps version number
-
-commit 4482df1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-19
-
- release v0.8
-
-commit 8a22def
-Merge: f21aa12 2dde04d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-19
-
- Merge branch 'master' into coverage
-
-commit 2dde04d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-19
-
- updates man page
-
-commit f21aa12
-Merge: 547d442 3c19a89
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-19
-
- Merge branch 'master' into coverage
-
-commit 3c19a89
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-19
-
- more micro optimizations
-
-commit 8cac12b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-18
-
- updates kseq.h
-
-commit 93fa5b7
-Merge: b90d408 e1d955d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-18
-
- Merge branch 'microopt'
-
-commit e1d955d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-18
-
- Revert "more use of FVC"
-
- This reverts commit 71218a5da1b1540165ac7081edc130d9201ceaf2.
-
-commit b90d408
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-18
-
- minor cleanup
-
-commit c7451af
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-18
-
- updates citation
-
-commit 547d442
-Merge: 13757e3 955eba9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-18
-
- Merge branch 'master' into coverage
-
-commit 955eba9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-15
-
- stop failing on very similar sequences
-
-commit 5e470a1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-12
-
- reduces memory usage
-
- The reverse-complement+forward string is only needed for the subjects in a comparison. Thus it can be computed on demand and freed afterwards. This reduces the memory from 3 byte per input nucleotide to 1+e where e depends on the number of threads.
-
-commit f713a0e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-12
-
- adds link to paper
-
-commit 396203e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-12-08
-
- removes further needless checks
-
-commit cf88d33
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- further simplifications
-
-commit 71218a5
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- more use of FVC
-
-commit 24d9e3e
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- simplifies condition
-
-commit 174c76d
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- removes some redundant checks
-
-commit efb8e9c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- simplify variables
-
-commit 72a6584
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- fixes wrong lookup on singleton intervals
-
-commit 18d5e8b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-12-07
-
- fixes serious typo
-
-commit 9df4a68
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-23
-
- first take at another optimization
-
-commit d7a0a28
-Merge: 44d82bd f9ce417
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-23
-
- Merge branch 'master' of https://github.com/kloetzl/andi
-
-commit 44d82bd
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-15
-
- replaces auto with proper types to support older compilers
-
-commit 13757e3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-20
-
- excludes libdivsufsort
-
-commit 62a4da6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-20
-
- fixes excludes for coveralls
-
-commit a7fe5d9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-17
-
- explicitly sets gcov path
-
-commit 366d145
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-17
-
- adds gcov build flags
-
-commit 622fa5c
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-17
-
- adds coveralls.io
-
-commit f9ce417
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-17
-
- Revert "adds libdivsufsort dir to includes for the unit tests"
-
- This reverts commit 3f7a6cf64c8565e5f5c4e21448e739b021babb22.
-
-commit 59568f8
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-15
-
- replaces auto with proper types to support older browsers
-
-commit ceca24b
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-15
-
- adds errno.h dependency
-
-commit c5d0af3
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-15
-
- bumps version number
-
-commit 8ea49c1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-14
-
- release v0.7.3
-
-commit 9618eae
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- adds travis build status to readme
-
-commit 75f99d9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- more travis trial and error
-
-commit 266bf8b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes travis library path
-
-commit d17cc3e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- use betters compilers
-
-commit ee93575
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes travis paths
-
-commit d12a1fa
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes travis scripts missing sudo
-
-commit 3ef0750
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes download link in travis build script
-
-commit 5ae938c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes travis syntax
-
-commit a8920ec
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- adds travis file
-
-commit 3f7a6cf
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- adds libdivsufsort dir to includes for the unit tests
-
-commit c6fc52e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes memory leak and other issues with test_fasta
-
-commit 26c1ba5
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes manpage
-
-commit 6f5133d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- fixes link for kseq.h
-
-commit 27301dd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- adds random unit tests
-
-commit 5dad58d
-Merge: 215d026 cb6b828
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-13
-
- Merge branch 'master' of github.com:EvolBioInf/andi
-
-commit cb6b828
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-11
-
- simplifies argument parsing
-
-commit 11328ae
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-11-11
-
- updates kseq.h
-
- This fixes not only compiler warnings but also an issue when reading from pipes. See https://github.com/lh3/seqtk/pull/43 for details.
-
-commit 215d026
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-10
-
- follow up commit
-
-commit 264bdf6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-10
-
- uses err.h instead of custom error messages
-
-commit f7055a1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-06
-
- adds another warning
-
-commit 9138257
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-06
-
- fixes warning being printed in any case
-
-commit 51211bf
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-06
-
- adds the vmatch script
-
- The vmatch script can be used to compare the performance of andi with vmatch. The latter can compute indexes and matches which then can be used to compute the anchor distance. Since vmatch is much slower then andi this last step is skipped.
-
-commit 9afc2c9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-06
-
- warns on failed estimations
-
-commit 60a7ffc
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-03
-
- fixes the changelog build
-
-commit 0f2125f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-03
-
- fixes ChangeLog reaction
-
-commit a3ccffd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-11-03
-
- release v0.7.2
-
- This is an insignificant testing release.
-
-commit 954a4a2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-30
-
- adds avg. anchor length to diagnostics
-
-commit 29b8851
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-27
-
- skips nucleotides known to be equal
-
-commit 8cb6b5b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-27
-
- fixes rare issue
-
- Let Q,S be sequences. If Q contains a nucleotide which S doesn't, before this commit the comparision would break at that point (or atleast in some cases). No it'll be treated as regular mismatch.
-
-commit beece1e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-27
-
- fixes race condition
-
-commit 02383fc
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-26
-
- removes useless initialization
-
-commit 10f8af4
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-26
-
- adds more input validation
-
-commit 8174d3d
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-26
-
- adds diagnostics
-
-commit 98414e5
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-26
-
- fixes function names to be more clear
-
-commit 3ca5764
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-26
-
- fixes ordering of members in lcp-intervals
-
-commit d52830d
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-25
-
- removes old code
-
-commit eadd193
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-24
-
- fixes more typos
-
-commit b27a7bf
-Author: Fabian Klötzl <fabian at kloetzl.info>
-Date: 2014-10-24
-
- fixes typos
-
-commit 0fe80ae
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-24
-
- bumps version number to v0.8-beta (again)
-
-commit 7295f5a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-24
-
- release v0.7.1
-
-commit e57593d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-24
-
- adds instructions for unit tests to readme
-
-commit ba4be59
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-24
-
- fixes dependency for GLIB2
-
- Previously GLIB2 was required for the unit tests. This commit make compilation of unit tests optional via a parameter for ./configure. By default its disabled.
-
-commit b8b5404
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-16
-
- bumps version to v0.8-beta
-
-commit efc51ee
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-16
-
- release v0.7
-
-commit ea1941c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-16
-
- updates man page
-
-commit d3d3cc0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-16
-
- fixes `make distcheck`
-
- The `make distcheck` command now completes successfully. To achieve that,
- the option subdir-objects hat to be disabled because of a bug in automake.
- See http://lists.gnu.org/archive/html/automake/2014-04/msg00003.html
- Hopefully that will not cause further issues in distributions of andi.
-
-commit 32536ce
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-16
-
- adds checks for stdint.h inttypes.h headers
-
-commit 1bde82b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-16
-
- fixes issue with AM_PROG_AR and old versions of autoconf
-
-commit 6d8685d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-14
-
- fixes some dist issues
-
-commit e9896c1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-14
-
- set default cache depth to 10
-
-commit bd7de82
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-14
-
- fixes caching
-
-commit 785e154
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-14
-
- optimizes no-rmqs
-
-commit a623882
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-09
-
- DRY
-
-commit 4c1fdd4
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-09
-
- reduces memory needs for fast mode
-
-commit 2987bf7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-09
-
- removes RMQ reference from help string
-
-commit 4718cd4
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-09
-
- adds docs
-
-commit cca056f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- annotates esa_init_CLD
-
-commit 8783b47
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- adds docs
-
-commit 6125618
-Merge: 821529a 31de193
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- Merge branch 'master' into no-rmq
-
-commit 821529a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- adds docs
-
-commit a474db7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- renames get*Interval functions
-
-commit 36eea19
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- removes ISA from ESA struct
-
-commit fd90671
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- removes RMQ from ESA struct
-
-commit 486e327
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- removes RMQ dependency
-
-commit 54215a0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-07
-
- removes various RMQ related code
-
-commit 31de193
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- fixes rare issue related to lcp-intervals with non-acgt suffixes
-
-commit 55fae2c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- fixes datatype
-
-commit 370f0a3
-Merge: f836305 39287a6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- Merge branch 'master' into no-rmq
-
-commit f836305
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- check result of esa_init_CLD
-
-commit 53af15b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- adds various tests
-
-commit c6e4522
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- fixes incorrect assertion
-
-commit 39287a6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-06
-
- catch error from malloc in cache initialization
-
-commit 21efc1c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-02
-
- fixes tests
-
-commit 848d7a3
-Merge: 6ac4f41 5047798
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-02
-
- Merge branch 'master' into no-rmq
-
- Conflicts:
- src/process.cpp
-
-commit 5047798
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-02
-
- fixes buffer underflow due to signedness error
-
-commit 6ac4f41
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-02
-
- uses the cached normq version
-
-commit 33301eb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-02
-
- adds LCP-interval finding strategy without RMQs
-
-commit cf03cfc
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-01
-
- adds guards for omp functions
-
-commit a9b0855
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-01
-
- updates help strings
-
-commit f7c212f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-01
-
- creates new io.cpp file
-
- * moves io functions into io.cpp
- * creates unified interface (FAIL,WARN) for errors
-
-commit 99bc3dd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-10-01
-
- adds --low-memory argument
-
-commit 53581d7
-Merge: 2810afb ef682bd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-29
-
- Merge branch 'master' into spacetime
-
-commit ef682bd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-29
-
- adds perf make target for Linux buildin perf tool
-
-commit 2810afb
-Merge: 16bad97 31baab2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-29
-
- Merge branch 'master' into spacetime
-
- Conflicts:
- src/process.cpp
-
-commit 31baab2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-29
-
- fixes some confusing API
-
-commit 2d28ef1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-25
-
- prints nicer error message
-
-commit 824d57b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-25
-
- speeds up hashing
-
-commit 8acea76
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-25
-
- fixes CACHE_LENGTH type
-
-commit 36dd292
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- ignores more test files
-
-commit 3f0150b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- adds unit tests for sequence manipulation
-
-commit 3f5d7fe
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- fixes wrong datatypes leading to memory corruption
-
-commit bc2bf3e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- fixes race condition
-
-commit b9cb1d3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- simplifies makefile
-
-commit 8c14ea3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- uses autoconf for glib flags
-
-commit f1104af
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- fixes make issues
-
-commit ba5871a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- fixes some make issues
-
-commit af2f8b2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-24
-
- ignore coverage files
-
-commit 9b3dd8f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-22
-
- adds unit tests for the cache
-
-commit 1396f46
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-22
-
- caches even more
-
-commit 1f75c78
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-22
-
- fixes caching
-
- These changes reenable caching. Now andi should be as fast as in version v0.6 and as accurate as in v0.5. (hopefully ;)
-
-commit 3af6e8a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- correctly handle lcp > 1
-
-commit ff4bc33
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- reenables caching which was effectively disabled in the last commit
-
-commit c29e2fe
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- fixes inaccurate results
-
- On filling the cache, beware of intervals whose LCP is longer than the current position. Previous to this commit incorrect paths in the suffix tree were followed and hence an incorrect cache was created. Now, for such cases, the code falls back to a non-cached search. The performance impact of this needs to be evaluated and might be due to changes in the future.
-
-commit 5ba4688
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- bumps version to 0.7-beta
-
-commit a363372
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- release v0.6
-
-commit fae1ac0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- fixes invalid read
-
- Valgrind reported an invalid read at this point. Googling suggests
- this might be a valgrind error. Still, casting solves the issue.
-
-commit d60ef86
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-19
-
- fixes various invalid read errors
-
-commit d2f9f53
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-18
-
- adds safety checks
-
-commit 611e3bf
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-18
-
- fixes use after free
-
-commit 16bad97
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-17
-
- changes parallelization
-
- Instead of computing all rows of the distance matrix simultaneously, we now fill a single row in parallel. At the moment this is slower, but uses less memory than the old method. In the future the user can pick either method via a (compile time) switch.
-
-commit 496eba0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-17
-
- adds profiling make target
-
-commit 0aa12d5
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-17
-
- fixes falsy coverage
-
-commit 8fe50e6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-17
-
- print additional coverage informatin on -v
-
-commit d2c900b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-17
-
- fixes unsafe comparison
-
-commit 36a037d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- inverts -p argument
-
-commit 7609f64
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- skip broken sequences
-
-commit 65a4f5f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- fixes further memory leak and nullptr deref.
-
-commit 622d2ec
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- fixes a memory leak
-
-commit 6177a9e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- renames *_seq -> seq_*
-
-commit 01b6fcc
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- adds docs
-
-commit 569d266
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- removes duplicate code
-
-commit 7803c6e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- removes deprecated functions
-
-commit 2454b97
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- clean up
-
-commit 373b2ae
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- ignore additional andi versions
-
-commit 602ab52
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-15
-
- adds build instructions for plain git repo.
-
-commit cabba9f
-Merge: decfc60 b85e8f9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- Merge branch 'cache'
-
-commit b85e8f9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- adds check in cache DFS
-
-commit 716958a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- fills the cache using a DFS
-
-commit b02964c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- quick exit on singleton intervals
-
-commit decfc60
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- fixes two possible memory leaks
-
-commit c60b4f6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- adds docs
-
-commit 9c92e8a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-04
-
- fixes code so it can be build on thymine
-
-commit 7ba1d36
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- implements RMQ caching
-
-commit 0b8a614
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- refactor ESA creation
-
-commit d0d431f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- renames dsa_init -> dsa_new
-
-commit d99262b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- canonicalize dsa_* function names
-
-commit 1ac0768
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- removes incorrect check
-
-commit 959fcfb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- updates RMQ library
-
- * update RMQ_succint to RMQ_improved. This results in faster programs
- at slightly more memory consumption.
- * fixes the memory leak by making the destructor of RMQ virtual.
- * updates Makefile, configure.ac and Readme
- * updates configure.ac and gitignore for non-posix archiver
-
-commit b4d6b15
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- bump version to v0.6-beta
-
-commit 149f8d2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- release v0.5
-
-commit 808fba6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- ignores compile file
-
-commit 2ee20d9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-09-01
-
- ignore sublime files
-
-commit b5d2115
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-08-08
-
- moves functions to allow inlining
-
-commit 2d8a089
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- simplifies code
-
- printf does not need the `l` in `%lf`. The type is double anyways.
-
-commit cf174a2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- forces execution of Changelog make rule
-
-commit 7996535
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- fixes typo
-
-commit 51fb88d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- enhances various docs
-
-commit 0a4f8a1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- improves docs in esa.h
-
-commit 9710462
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- improves docs for printDistMatrix
-
-commit 79ed6ce
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- adds test to gitignore
-
-commit 37d4096
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- adds docs for minAnchorLength
-
-commit 77a2463
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- improves docs slightly
-
-commit b963e25
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- fixes undefined behaviour
-
-commit 226c6a3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- removes obsolete -s commandline argument
-
-commit 3fe143e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- fixes instructions for building the code docs
-
-commit 646875b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- fixes code docs not building
-
-commit 8bbdd3f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- return nan also in --raw mode
-
-commit 613df03
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- improves readme
-
-commit a43bf35
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- removes some TODOs
-
-commit e2836dc
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-30
-
- adds changelog
-
- * The changelog is automatically generated from git
-
-commit bdc26c0
-Author: kloetzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-26
-
- adds data sets to readme
-
-commit 06a06a3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-25
-
- changes to our own binomial coeff. implementation
-
- * Removes dependecy for GSL
- * Use our own implementation for computing the
- binomial coefficient.
-
-commit e34763f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-25
-
- fixes configure script not adding -ldivsufsort
-
- * closes issue #1
-
-commit 0c4603a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-25
-
- improves autoconf check for libdivsufsort
-
- * We now also check for the existence of the header file.
- * If the lib if not properly installed we now abort compilation
- with an error.
-
-commit 997faf6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- updates readme
-
- * adds simK tool
- * improves licensing paragraph
-
-commit 92ac7cd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- adds maf2phy.awk script
-
- This script can convert the *mutation annotation format* to
- PHYLIP format, as stated in the accompanying paper.
-
-commit 907dfdc
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- improves readme
-
- The readme is optimized to provide a nice project overview when
- seen via GitHub.
-
-commit 1686f39
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- auto generate make file
-
-commit 612ea9d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- bumps version number
-
-commit 1fd6351
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- release v0.4
-
-commit a6b6a17
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-23
-
- changing anchor length calculation
-
- replacing the formula for the minimum anchor length with formula (4)
- from Haubold et al. (2009)
-
-commit 851e94a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-19
-
- improves man page
-
-commit 32db374
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-19
-
- updates documentation to better explain -p
-
-commit a3c46ac
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-19
-
- changes default -p value to 0.95
-
- For real this time.
-
-commit d140650
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-19
-
- Revert "changes default -p value to 0.95"
-
- This reverts commit e02845f9e0bb93f25d56d16d07c19b6c863f86cd.
-
-commit e02845f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-19
-
- changes default -p value to 0.95
-
-commit 8e39cc7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- improves readme
-
-commit 612984a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- adds configure to gitignore
-
-commit 2796fe8
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- improves autoconf files
-
-commit 196c907
-Merge: 76910b1 f6a7569
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- Merge branch 'master' into autoconf
-
-commit f6a7569
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- correct the authors name
-
-commit 76910b1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- improves man page
-
-commit 74c01b7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- changes version number
-
-commit 06b0821
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- removes automatically generated file
-
-commit e6b23b0
-Merge: f25d3c3 f1ab00c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- Merge branch 'master' into autoconf
-
-commit f1ab00c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- pretty print filenames in join mode
-
-commit f25d3c3
-Merge: 59acc79 efc335f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- Merge branch 'master' into autoconf
-
- Conflicts:
- src/Makefile
-
-commit efc335f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- catches another rare error
-
-commit cff7fea
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- validate input
-
-commit 5458c2e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-18
-
- fixes join mode
-
- This is a rewrite of the join mode. The changes include:
-
- * Rather than iteratively using `asprintf` to create the new long sequence
- we now call `malloc` once.
- * Ditch the crude handwritten implementation of a dynamically growing
- array. Instead a C wrapper for `std::vector<seq_t>` is used.
- * The name of a joined sequence is now the filename.
- * Of a sequence name only the first nine characters get printed.
- * Adds and fixes documentation all over the place.
- * Renames `sequence.c` to `sequence.cpp` to reflect the fact that its
- code is actually C++.
-
-commit 59acc79
-Merge: 83e0891 28da4c0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-16
-
- Merge branch 'master' into autoconf
-
-commit 28da4c0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-16
-
- adds docs
-
-commit 11656a8
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-12
-
- changes default -p value to 0.6
-
-commit 03ff31c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-12
-
- removes needless define and removes warning
-
-commit aa6e559
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-12
-
- adds join mode
-
- The join mode treats every sequences from a file as part of one genome. It does
- so by appending the sequences to each other with a separator character in between.
- This is useful if contigs of one organism are kept in one file and need to be
- compared to another organism.
-
- The join mode is activated via --join or -j and expects at least one filename
- to be passed via command line arguments.
-
-commit 83e0891
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- adds missing to gitignore
-
-commit 42b818d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- improves readme
-
-commit 541e982
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- removes missing file
-
-commit bb86846
-Merge: d0a877d d18f5f1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- Merge branch 'master' into autoconf
-
-commit d18f5f1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- fixes low precision of printed results
-
- If the distance matrix contains values smaller than 0.001
- we now use scientific notation for the output to increase the
- presicion.
-
-commit 6160450
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- fixes NaN result for nearly identical sequences
-
-commit e3eb46c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- fixes acknowledgements
-
-commit ed959c3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- adds acknowledgements
-
-commit f02a2a1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-11
-
- improves output
-
- Now the default values for all parameters are printed on --help.
-
-commit 25b0838
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-05
-
- fixes result for identical sequences
-
-commit 50e94f1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-05
-
- changes names to be printed left adjusted
-
-commit d0a877d
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-05
-
- changes version number to conform to debian standards
-
-commit ed67160
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-05
-
- makes stripping mandatory and ignores case
-
- The stripping introduced in the last commit is now done automatically. Hence
- the option --strip is removed. Still, a warning is issued if characters other
- than [acgtACGT] were contained in the input. Also the case of the input is now
- being ignored.
-
-commit 8966fb2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-05
-
- adds various files to build process
-
-commit 3beb749
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-05
-
- adds strip option
-
-commit 64a2a77
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- adds rough man page
-
-commit f204d7e
-Merge: 0a78ab2 61b04d5
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- Merge branch 'master' into autoconf
-
-commit 0a78ab2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- prepares for better documentation
-
-commit a1a87f8
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- cleans up makefiles
-
-commit 3f73bb8
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- adds missing file
-
-commit 9acb51e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- fixes readme to reflect autoconf changes
-
-commit 4cabef5
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- generate a README from README.md to satisfy autoconf
-
-commit 61b04d5
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- improves help string
-
-commit da3af7b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- removes the option to use different strategies
-
-commit d5c8452
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- removes option for single stranded comparision
-
-commit 0b55dee
-Merge: 7d6a0eb ae812b9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- Merge branch 'master' into autoconf
-
- Conflicts:
- src/Makefile
-
-commit 7d6a0eb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- improves .gitignore to ignore various autoconf files
-
-commit 82586e0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- adds configure.ac script
-
-commit 3bc6895
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- adds configure script
-
-commit e24a215
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- adds GNU style files
-
-commit 9d326f9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- switches from manual make files to automake
-
-commit ae812b9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- removes resolved TODOs
-
-commit 0e7a48a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- adds gc-content calculation
-
-commit ff9166a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-04
-
- removes libdivsufsort64 dependency
-
-commit bae0912
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-02
-
- renames files for autoconf
-
- With autoconf, we can no longer compile .c files using CXX. They
- have to have the ending .cpp or an error will be thrown. Also the
- Makefile is now generated by automake.
-
-commit e800c53
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-02
-
- removing test file
-
-commit 175f2d9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-02
-
- renames np to andi
-
-commit 6e6f855
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-02
-
- increases the max number of sequences
-
-commit f3d67dd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-06-02
-
- fixes help string
-
-commit 0862a0a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- bumps version number
-
-commit 9a74c1b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- v0.3
-
-commit 457f7f0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- fixes typo in docs
-
-commit d52f433
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- further cleanup
-
-commit 6b315f7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- removes code rendered unneccessary by the previous commit
-
-commit d8218bd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- removes simple strategy
-
-commit b4f2498
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- merged optimization
-
-commit 6f247a8
-Merge: b1a7657 687fe1b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- Merge branch 'optimization'
-
-commit b1a7657
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- fixes random anchor propability
-
- The -p switch now resembles the certainty that a pair of anchors
- is not random. This takes into account that both anchors of a pair
- may be independently found by chance alone. p=0.95 is the new
- default value.
-
-commit 687fe1b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- saving yet another RMQ
-
-commit b71b3e4
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- corrects the threshhold computation
-
-commit 4c9e492
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- adds anchor length calculation
-
-commit cdcc38b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-28
-
- changes default strategy to anchor
-
-commit cbc990c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- improves code and docs
-
-commit 8abb51b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- improves docs
-
-commit 1bcefe3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- improves code and docs
-
-commit 633c56c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- improves readme
-
-commit d62338b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- removes sophisticated strategy
-
-commit b512a40
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- adds readme
-
-commit 688302f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- adds more docs
-
-commit 533ef97
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-26
-
- changes -c to -t and CORES to THREADS
-
-commit 1e7bc51
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-22
-
- adds docs
-
-commit 3dbdd74
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-22
-
- removes check for NULL.
-
- free(3) can totaly work with NULL values. Stop checking for that.
-
-commit 66efa76
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-22
-
- removes inc, check and window strategy
-
-commit 03020f2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-21
-
- create symmetric distance matrix and print N
-
-commit e78d80c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-21
-
- adds anchor strategy
-
-commit de01ee2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-21
-
- adds docs and debug information
-
-commit 156bc46
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-19
-
- adds docs make target
-
-commit 111b306
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- enhances documentation
-
-commit 473ddbf
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- adds documentation via doxygen
-
-commit 447d85e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- nicer help string
-
-commit 41c53f0
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- removes abundant variable
-
-commit 8822d26
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- adds strategies to help string
-
-commit b5fda92
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- uses better api methods
-
-commit 26a9a56
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- fixes function declaration
-
-commit 3cff29c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-15
-
- enhances program arguments
-
-commit b9a0320
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- fixes wrong lookahead
-
-commit eae68b5
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- fixes comparisions and adds variable number of mismatches
-
-commit 09d8271
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- break after a snp
-
-commit d18b14f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- enhances sophisticated strategy
-
-commit 1ff08a7
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- adds 'sophisticated' distance method
-
-commit 4e0bf24
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- adds dist_check method
-
-commit d8528f3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-14
-
- moves catcomp() and revcomp()
-
-commit 784c4d2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- bumps version number
-
-commit 0c6e8f3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- version 0.2
-
-commit e480717
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- fixes incompatible compile flags
-
-commit 3aa3e69
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- fixes help string
-
-commit 3747d87
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- makes double stranded comparision the default
-
- Instead of using -d to activate double stranded comparision, -D can
- be used to disable it. Single stranded comparison is faster but
- less accurate.
-
-commit 1c06e42
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- adds rough neighbouhood strategy
-
-commit 9b0c763
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- prefer const pointers
-
-commit b1163eb
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- fixes wrong types and debug information in dist_inc()
-
-commit 07667de
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- removes old headers
-
-commit 9049b81
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- removes unused variable
-
-commit 4f6a4b6
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- adds another file to the clean command
-
-commit 50e8c2e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- updates gitignore
-
-commit e28a0af
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-12
-
- removes testRMQ binary file
-
-commit 94fcd06
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- use a search window of 10 for the inc strategy
-
-commit b3a768a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- removes uninteresting test files
-
-commit 5e7ad4a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- removes yet another useless file
-
-commit 019d0e9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- removes and untracks old files
-
-commit fed5793
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- bumps version number
-
-commit 51de1d1
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- simplifies code
-
-commit f189a0c
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- removes extra semicolon
-
-commit ddbf36a
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- adds version
-
-commit f60397f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-08
-
- simplifies inc strategy
-
-commit 4688690
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- fixes wrong types
-
-commit 59c06a3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- fixes wrong corection
-
-commit 95f8a69
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- adds more docs
-
-commit 1fe82e9
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- adds docs
-
-commit cf71d8f
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- adds documentation and fixes types
-
-commit 283acfd
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- removes even more lines of unused code
-
-commit e160808
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- uses correct types
-
-commit 9105ce4
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- removes legacy code
-
-commit e8427e3
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- removes old code
-
-commit 9bef601
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-07
-
- adds comments
-
-commit 700200e
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- removes unneccessary code
-
-commit bb97a07
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- optimize for speed
-
-commit 0685e12
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- removes .o files
-
-commit aa3ff1b
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- adds .gitignore
-
-commit 0262461
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- removed profiling files
-
-commit f79e294
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- only use 32 bit and other optimizations
-
-commit bdc5db2
-Author: Fabian Klötzl <kloetzl at evolbio.mpg.de>
-Date: 2014-05-05
-
- adds files
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diff --git a/README b/README
deleted file mode 100644
index 9be208b..0000000
--- a/README
+++ /dev/null
@@ -1,66 +0,0 @@
-[](https://travis-ci.org/EvolBioInf/andi) [](https://coveralls.io/r/EvolBioInf/andi?branch=master)
-
-# About
-
-This is the `andi` program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because `andi` does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
-
-This readme covers all necessary instructions for the impatient to get `andi` up and running. For extensive instructions please consult the [manual](andi-manual.pdf).
-
-
-# Build Instructions
-
-For the latest [stable release](https://github.com/EvolBioInf/andi/releases) of `andi` download the tar ball. If you'd like to contribute to this software, feel free to create a fork of our [git repository](https://github.com/EvolBioInf/andi) and send pull requests.
-
-
-## Prerequisites
-
-This program has the following external dependency: [libdivsufsort](https://code.google.com/p/libdivsufsort/). Please make sure you installed `libdivsufsort` before attempting a build. If you did get the source, not as a tarball, but straight from the git repository, you will also need the autotools. Run `autoreconf -i` to generate the configure script and continue with the next step.
-
-
-## Compiling
-
-Assuming you have installed all prerequisites, building is as easy as follows.
-
- $ ./configure
- $ make
- $ make install
-
-Excessive build instructions are located in `INSTALL`. If the build was successful you can get the usage instructions via `--help` or the man page.
-
- $ andi --help
- $ man andi
-
-You can use simply `andi` with your genomes in `FASTA` format.
-
- $ andi S1.fasta S2.fasta
- 2
- S1 0.0 0.1
- s2 0.1 0.0
-
-From this distance matrix the phylogeny can be inferred via neighbor-joining. Check the [manual](andi-manual.pdf). for a more thorough description.
-
-
-# Links and Additional Resources
-
-The release of this software is accompanied by a paper from [Haubold et al.](http://bioinformatics.oxfordjournals.org/content/31/8/1169). It explains the used *anchor distance* strategy in great detail. The `maf2phy.awk` script used in the validation process is located under `scripts`. Simulations were done using our own [simK](http://guanine.evolbio.mpg.de/bioBox/) tool.
-
-## Data Sets
-
-1. 29. E. coli strains: [data](http://guanine.evolbio.mpg.de/andi/eco29.fasta.gz)
-2. 109 E. coli ST131 strains ([paper](http://www.pnas.org/content/early/2014/03/28/1322678111.abstract)):
- * [99 newly sequenced strains](https://github.com/BeatsonLab-MicrobialGenomics/ST131_99)
- * [10 previously published strains](http://guanine.evolbio.mpg.de/andi/st131_extra.tgz)
-3. 3085 Streptococcus pneumoniae strains ([paper](http://www.nature.com/ng/journal/v46/n3/full/ng.2895.html)): ftp://ftp.sanger.ac.uk/pub/pathogens/Streptococcus/pneumoniae/Maela_assemblies.tgz
-
-## License
-
-Copyright © 2014, 2015 Fabian Klötzl
-License GPLv3+: GNU GPL version 3 or later.
-
-This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. The full license text is available at <http://gnu.org/licenses/gpl.html>.
-
-Some files may be licensed differently.
-
-## Contact
-
-In case of bugs or unexpected errors don't hesitate to send me a mail: kloetzl at evolbio.mpg.de
diff --git a/aclocal.m4 b/aclocal.m4
deleted file mode 100644
index ec10480..0000000
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+++ /dev/null
@@ -1,1370 +0,0 @@
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-# with or without modifications, as long as this notice is preserved.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY, to the extent permitted by law; without
-# even the implied warranty of MERCHANTABILITY or FITNESS FOR A
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-# One issue with vendor 'install' (even GNU) is that you can't
-# specify the program used to strip binaries. This is especially
-# annoying in cross-compiling environments, where the build's strip
-# is unlikely to handle the host's binaries.
-# Fortunately install-sh will honor a STRIPPROG variable, so we
-# always use install-sh in "make install-strip", and initialize
-# STRIPPROG with the value of the STRIP variable (set by the user).
-AC_DEFUN([AM_PROG_INSTALL_STRIP],
-[AC_REQUIRE([AM_PROG_INSTALL_SH])dnl
-# Installed binaries are usually stripped using 'strip' when the user
-# run "make install-strip". However 'strip' might not be the right
-# tool to use in cross-compilation environments, therefore Automake
-# will honor the 'STRIP' environment variable to overrule this program.
-dnl Don't test for $cross_compiling = yes, because it might be 'maybe'.
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- AC_CHECK_TOOL([STRIP], [strip], :)
-fi
-INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s"
-AC_SUBST([INSTALL_STRIP_PROGRAM])])
-
-# Copyright (C) 2006-2013 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# _AM_SUBST_NOTMAKE(VARIABLE)
-# ---------------------------
-# Prevent Automake from outputting VARIABLE = @VARIABLE@ in Makefile.in.
-# This macro is traced by Automake.
-AC_DEFUN([_AM_SUBST_NOTMAKE])
-
-# AM_SUBST_NOTMAKE(VARIABLE)
-# --------------------------
-# Public sister of _AM_SUBST_NOTMAKE.
-AC_DEFUN([AM_SUBST_NOTMAKE], [_AM_SUBST_NOTMAKE($@)])
-
-# Check how to create a tarball. -*- Autoconf -*-
-
-# Copyright (C) 2004-2013 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# _AM_PROG_TAR(FORMAT)
-# --------------------
-# Check how to create a tarball in format FORMAT.
-# FORMAT should be one of 'v7', 'ustar', or 'pax'.
-#
-# Substitute a variable $(am__tar) that is a command
-# writing to stdout a FORMAT-tarball containing the directory
-# $tardir.
-# tardir=directory && $(am__tar) > result.tar
-#
-# Substitute a variable $(am__untar) that extract such
-# a tarball read from stdin.
-# $(am__untar) < result.tar
-#
-AC_DEFUN([_AM_PROG_TAR],
-[# Always define AMTAR for backward compatibility. Yes, it's still used
-# in the wild :-( We should find a proper way to deprecate it ...
-AC_SUBST([AMTAR], ['$${TAR-tar}'])
-
-# We'll loop over all known methods to create a tar archive until one works.
-_am_tools='gnutar m4_if([$1], [ustar], [plaintar]) pax cpio none'
-
-m4_if([$1], [v7],
- [am__tar='$${TAR-tar} chof - "$$tardir"' am__untar='$${TAR-tar} xf -'],
-
- [m4_case([$1],
- [ustar],
- [# The POSIX 1988 'ustar' format is defined with fixed-size fields.
- # There is notably a 21 bits limit for the UID and the GID. In fact,
- # the 'pax' utility can hang on bigger UID/GID (see automake bug#8343
- # and bug#13588).
- am_max_uid=2097151 # 2^21 - 1
- am_max_gid=$am_max_uid
- # The $UID and $GID variables are not portable, so we need to resort
- # to the POSIX-mandated id(1) utility. Errors in the 'id' calls
- # below are definitely unexpected, so allow the users to see them
- # (that is, avoid stderr redirection).
- am_uid=`id -u || echo unknown`
- am_gid=`id -g || echo unknown`
- AC_MSG_CHECKING([whether UID '$am_uid' is supported by ustar format])
- if test $am_uid -le $am_max_uid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi
- AC_MSG_CHECKING([whether GID '$am_gid' is supported by ustar format])
- if test $am_gid -le $am_max_gid; then
- AC_MSG_RESULT([yes])
- else
- AC_MSG_RESULT([no])
- _am_tools=none
- fi],
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- [pax],
- [],
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- [m4_fatal([Unknown tar format])])
-
- AC_MSG_CHECKING([how to create a $1 tar archive])
-
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- _am_tools=${am_cv_prog_tar_$1-$_am_tools}
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- case $_am_tool in
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- AM_RUN_LOG([$_am_tar --version]) && break
- done
- am__tar="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$$tardir"'
- am__tar_="$_am_tar --format=m4_if([$1], [pax], [posix], [$1]) -chf - "'"$tardir"'
- am__untar="$_am_tar -xf -"
- ;;
- plaintar)
- # Must skip GNU tar: if it does not support --format= it doesn't create
- # ustar tarball either.
- (tar --version) >/dev/null 2>&1 && continue
- am__tar='tar chf - "$$tardir"'
- am__tar_='tar chf - "$tardir"'
- am__untar='tar xf -'
- ;;
- pax)
- am__tar='pax -L -x $1 -w "$$tardir"'
- am__tar_='pax -L -x $1 -w "$tardir"'
- am__untar='pax -r'
- ;;
- cpio)
- am__tar='find "$$tardir" -print | cpio -o -H $1 -L'
- am__tar_='find "$tardir" -print | cpio -o -H $1 -L'
- am__untar='cpio -i -H $1 -d'
- ;;
- none)
- am__tar=false
- am__tar_=false
- am__untar=false
- ;;
- esac
-
- # If the value was cached, stop now. We just wanted to have am__tar
- # and am__untar set.
- test -n "${am_cv_prog_tar_$1}" && break
-
- # tar/untar a dummy directory, and stop if the command works.
- rm -rf conftest.dir
- mkdir conftest.dir
- echo GrepMe > conftest.dir/file
- AM_RUN_LOG([tardir=conftest.dir && eval $am__tar_ >conftest.tar])
- rm -rf conftest.dir
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- AM_RUN_LOG([$am__untar <conftest.tar])
- AM_RUN_LOG([cat conftest.dir/file])
- grep GrepMe conftest.dir/file >/dev/null 2>&1 && break
- fi
- done
- rm -rf conftest.dir
-
- AC_CACHE_VAL([am_cv_prog_tar_$1], [am_cv_prog_tar_$1=$_am_tool])
- AC_MSG_RESULT([$am_cv_prog_tar_$1])])
-
-AC_SUBST([am__tar])
-AC_SUBST([am__untar])
-]) # _AM_PROG_TAR
-
-m4_include([m4/ax_cxx_compile_stdcxx_11.m4])
diff --git a/ar-lib b/ar-lib
deleted file mode 100755
index fe2301e..0000000
--- a/ar-lib
+++ /dev/null
@@ -1,270 +0,0 @@
-#! /bin/sh
-# Wrapper for Microsoft lib.exe
-
-me=ar-lib
-scriptversion=2012-03-01.08; # UTC
-
-# Copyright (C) 2010-2013 Free Software Foundation, Inc.
-# Written by Peter Rosin <peda at lysator.liu.se>.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake at gnu.org> or send patches to
-# <automake-patches at gnu.org>.
-
-
-# func_error message
-func_error ()
-{
- echo "$me: $1" 1>&2
- exit 1
-}
-
-file_conv=
-
-# func_file_conv build_file
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts.
-func_file_conv ()
-{
- file=$1
- case $file in
- / | /[!/]*) # absolute file, and not a UNC file
- if test -z "$file_conv"; then
- # lazily determine how to convert abs files
- case `uname -s` in
- MINGW*)
- file_conv=mingw
- ;;
- CYGWIN*)
- file_conv=cygwin
- ;;
- *)
- file_conv=wine
- ;;
- esac
- fi
- case $file_conv in
- mingw)
- file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
- ;;
- cygwin)
- file=`cygpath -m "$file" || echo "$file"`
- ;;
- wine)
- file=`winepath -w "$file" || echo "$file"`
- ;;
- esac
- ;;
- esac
-}
-
-# func_at_file at_file operation archive
-# Iterate over all members in AT_FILE performing OPERATION on ARCHIVE
-# for each of them.
-# When interpreting the content of the @FILE, do NOT use func_file_conv,
-# since the user would need to supply preconverted file names to
-# binutils ar, at least for MinGW.
-func_at_file ()
-{
- operation=$2
- archive=$3
- at_file_contents=`cat "$1"`
- eval set x "$at_file_contents"
- shift
-
- for member
- do
- $AR -NOLOGO $operation:"$member" "$archive" || exit $?
- done
-}
-
-case $1 in
- '')
- func_error "no command. Try '$0 --help' for more information."
- ;;
- -h | --h*)
- cat <<EOF
-Usage: $me [--help] [--version] PROGRAM ACTION ARCHIVE [MEMBER...]
-
-Members may be specified in a file named with @FILE.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "$me, version $scriptversion"
- exit $?
- ;;
-esac
-
-if test $# -lt 3; then
- func_error "you must specify a program, an action and an archive"
-fi
-
-AR=$1
-shift
-while :
-do
- if test $# -lt 2; then
- func_error "you must specify a program, an action and an archive"
- fi
- case $1 in
- -lib | -LIB \
- | -ltcg | -LTCG \
- | -machine* | -MACHINE* \
- | -subsystem* | -SUBSYSTEM* \
- | -verbose | -VERBOSE \
- | -wx* | -WX* )
- AR="$AR $1"
- shift
- ;;
- *)
- action=$1
- shift
- break
- ;;
- esac
-done
-orig_archive=$1
-shift
-func_file_conv "$orig_archive"
-archive=$file
-
-# strip leading dash in $action
-action=${action#-}
-
-delete=
-extract=
-list=
-quick=
-replace=
-index=
-create=
-
-while test -n "$action"
-do
- case $action in
- d*) delete=yes ;;
- x*) extract=yes ;;
- t*) list=yes ;;
- q*) quick=yes ;;
- r*) replace=yes ;;
- s*) index=yes ;;
- S*) ;; # the index is always updated implicitly
- c*) create=yes ;;
- u*) ;; # TODO: don't ignore the update modifier
- v*) ;; # TODO: don't ignore the verbose modifier
- *)
- func_error "unknown action specified"
- ;;
- esac
- action=${action#?}
-done
-
-case $delete$extract$list$quick$replace,$index in
- yes,* | ,yes)
- ;;
- yesyes*)
- func_error "more than one action specified"
- ;;
- *)
- func_error "no action specified"
- ;;
-esac
-
-if test -n "$delete"; then
- if test ! -f "$orig_archive"; then
- func_error "archive not found"
- fi
- for member
- do
- case $1 in
- @*)
- func_at_file "${1#@}" -REMOVE "$archive"
- ;;
- *)
- func_file_conv "$1"
- $AR -NOLOGO -REMOVE:"$file" "$archive" || exit $?
- ;;
- esac
- done
-
-elif test -n "$extract"; then
- if test ! -f "$orig_archive"; then
- func_error "archive not found"
- fi
- if test $# -gt 0; then
- for member
- do
- case $1 in
- @*)
- func_at_file "${1#@}" -EXTRACT "$archive"
- ;;
- *)
- func_file_conv "$1"
- $AR -NOLOGO -EXTRACT:"$file" "$archive" || exit $?
- ;;
- esac
- done
- else
- $AR -NOLOGO -LIST "$archive" | sed -e 's/\\/\\\\/g' | while read member
- do
- $AR -NOLOGO -EXTRACT:"$member" "$archive" || exit $?
- done
- fi
-
-elif test -n "$quick$replace"; then
- if test ! -f "$orig_archive"; then
- if test -z "$create"; then
- echo "$me: creating $orig_archive"
- fi
- orig_archive=
- else
- orig_archive=$archive
- fi
-
- for member
- do
- case $1 in
- @*)
- func_file_conv "${1#@}"
- set x "$@" "@$file"
- ;;
- *)
- func_file_conv "$1"
- set x "$@" "$file"
- ;;
- esac
- shift
- shift
- done
-
- if test -n "$orig_archive"; then
- $AR -NOLOGO -OUT:"$archive" "$orig_archive" "$@" || exit $?
- else
- $AR -NOLOGO -OUT:"$archive" "$@" || exit $?
- fi
-
-elif test -n "$list"; then
- if test ! -f "$orig_archive"; then
- func_error "archive not found"
- fi
- $AR -NOLOGO -LIST "$archive" || exit $?
-fi
diff --git a/compile b/compile
deleted file mode 100755
index 531136b..0000000
--- a/compile
+++ /dev/null
@@ -1,347 +0,0 @@
-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
-# Written by Tom Tromey <tromey at cygnus.com>.
-#
-# This program 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, or (at your option)
-# any later version.
-#
-# This program 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 <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <bug-automake at gnu.org> or send patches to
-# <automake-patches at gnu.org>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order. Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" "" $nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
- file=$1
- case $file in
- / | /[!/]*) # absolute file, and not a UNC file
- if test -z "$file_conv"; then
- # lazily determine how to convert abs files
- case `uname -s` in
- MINGW*)
- file_conv=mingw
- ;;
- CYGWIN*)
- file_conv=cygwin
- ;;
- *)
- file_conv=wine
- ;;
- esac
- fi
- case $file_conv/,$2, in
- *,$file_conv,*)
- ;;
- mingw/*)
- file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
- ;;
- cygwin/*)
- file=`cygpath -m "$file" || echo "$file"`
- ;;
- wine/*)
- file=`winepath -w "$file" || echo "$file"`
- ;;
- esac
- ;;
- esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
- func_file_conv "$1"
- if test -z "$lib_path"; then
- lib_path=$file
- else
- lib_path="$lib_path;$file"
- fi
- linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
- lib=$1
- found=no
- save_IFS=$IFS
- IFS=';'
- for dir in $lib_path $LIB
- do
- IFS=$save_IFS
- if $shared && test -f "$dir/$lib.dll.lib"; then
- found=yes
- lib=$dir/$lib.dll.lib
- break
- fi
- if test -f "$dir/$lib.lib"; then
- found=yes
- lib=$dir/$lib.lib
- break
- fi
- if test -f "$dir/lib$lib.a"; then
- found=yes
- lib=$dir/lib$lib.a
- break
- fi
- done
- IFS=$save_IFS
-
- if test "$found" != yes; then
- lib=$lib.lib
- fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
- # Assume a capable shell
- lib_path=
- shared=:
- linker_opts=
- for arg
- do
- if test -n "$eat"; then
- eat=
- else
- case $1 in
- -o)
- # configure might choose to run compile as 'compile cc -o foo foo.c'.
- eat=1
- case $2 in
- *.o | *.[oO][bB][jJ])
- func_file_conv "$2"
- set x "$@" -Fo"$file"
- shift
- ;;
- *)
- func_file_conv "$2"
- set x "$@" -Fe"$file"
- shift
- ;;
- esac
- ;;
- -I)
- eat=1
- func_file_conv "$2" mingw
- set x "$@" -I"$file"
- shift
- ;;
- -I*)
- func_file_conv "${1#-I}" mingw
- set x "$@" -I"$file"
- shift
- ;;
- -l)
- eat=1
- func_cl_dashl "$2"
- set x "$@" "$lib"
- shift
- ;;
- -l*)
- func_cl_dashl "${1#-l}"
- set x "$@" "$lib"
- shift
- ;;
- -L)
- eat=1
- func_cl_dashL "$2"
- ;;
- -L*)
- func_cl_dashL "${1#-L}"
- ;;
- -static)
- shared=false
- ;;
- -Wl,*)
- arg=${1#-Wl,}
- save_ifs="$IFS"; IFS=','
- for flag in $arg; do
- IFS="$save_ifs"
- linker_opts="$linker_opts $flag"
- done
- IFS="$save_ifs"
- ;;
- -Xlinker)
- eat=1
- linker_opts="$linker_opts $2"
- ;;
- -*)
- set x "$@" "$1"
- shift
- ;;
- *.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
- func_file_conv "$1"
- set x "$@" -Tp"$file"
- shift
- ;;
- *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
- func_file_conv "$1" mingw
- set x "$@" "$file"
- shift
- ;;
- *)
- set x "$@" "$1"
- shift
- ;;
- esac
- fi
- shift
- done
- if test -n "$linker_opts"; then
- linker_opts="-link$linker_opts"
- fi
- exec "$@" $linker_opts
- exit 1
-}
-
-eat=
-
-case $1 in
- '')
- echo "$0: No command. Try '$0 --help' for more information." 1>&2
- exit 1;
- ;;
- -h | --h*)
- cat <<\EOF
-Usage: compile [--help] [--version] PROGRAM [ARGS]
-
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
-arguments, and rename the output as expected.
-
-If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "compile $scriptversion"
- exit $?
- ;;
- cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
- func_cl_wrapper "$@" # Doesn't return...
- ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
- if test -n "$eat"; then
- eat=
- else
- case $1 in
- -o)
- # configure might choose to run compile as 'compile cc -o foo foo.c'.
- # So we strip '-o arg' only if arg is an object.
- eat=1
- case $2 in
- *.o | *.obj)
- ofile=$2
- ;;
- *)
- set x "$@" -o "$2"
- shift
- ;;
- esac
- ;;
- *.c)
- cfile=$1
- set x "$@" "$1"
- shift
- ;;
- *)
- set x "$@" "$1"
- shift
- ;;
- esac
- fi
- shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
- # If no '-o' option was seen then we might have been invoked from a
- # pattern rule where we don't need one. That is ok -- this is a
- # normal compilation that the losing compiler can handle. If no
- # '.c' file was seen then we are probably linking. That is also
- # ok.
- exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file. Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
- if mkdir "$lockdir" >/dev/null 2>&1; then
- break
- fi
- sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
- test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
- test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:
diff --git a/configure b/configure
deleted file mode 100755
index 4c02a85..0000000
--- a/configure
+++ /dev/null
@@ -1,7968 +0,0 @@
-#! /bin/sh
-# Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.69 for andi 0.9.4.
-#
-#
-# Copyright (C) 1992-1996, 1998-2012 Free Software Foundation, Inc.
-#
-#
-# This configure script is free software; the Free Software Foundation
-# gives unlimited permission to copy, distribute and modify it.
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
-
-# Be more Bourne compatible
-DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
- emulate sh
- NULLCMD=:
- # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
-else
- case `(set -o) 2>/dev/null` in #(
- *posix*) :
- set -o posix ;; #(
- *) :
- ;;
-esac
-fi
-
-
-as_nl='
-'
-export as_nl
-# Printing a long string crashes Solaris 7 /usr/bin/printf.
-as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
- && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
- as_echo='print -r --'
- as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
- as_echo='printf %s\n'
- as_echo_n='printf %s'
-else
- if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
- as_echo_n='/usr/ucb/echo -n'
- else
- as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
- as_echo_n_body='eval
- arg=$1;
- case $arg in #(
- *"$as_nl"*)
- expr "X$arg" : "X\\(.*\\)$as_nl";
- arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
- esac;
- expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
- '
- export as_echo_n_body
- as_echo_n='sh -c $as_echo_n_body as_echo'
- fi
- export as_echo_body
- as_echo='sh -c $as_echo_body as_echo'
-fi
-
-# The user is always right.
-if test "${PATH_SEPARATOR+set}" != set; then
- PATH_SEPARATOR=:
- (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
- (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
- PATH_SEPARATOR=';'
- }
-fi
-
-
-# IFS
-# We need space, tab and new line, in precisely that order. Quoting is
-# there to prevent editors from complaining about space-tab.
-# (If _AS_PATH_WALK were called with IFS unset, it would disable word
-# splitting by setting IFS to empty value.)
-IFS=" "" $as_nl"
-
-# Find who we are. Look in the path if we contain no directory separator.
-as_myself=
-case $0 in #((
- *[\\/]* ) as_myself=$0 ;;
- *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
- done
-IFS=$as_save_IFS
-
- ;;
-esac
-# We did not find ourselves, most probably we were run as `sh COMMAND'
-# in which case we are not to be found in the path.
-if test "x$as_myself" = x; then
- as_myself=$0
-fi
-if test ! -f "$as_myself"; then
- $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- exit 1
-fi
-
-# Unset variables that we do not need and which cause bugs (e.g. in
-# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1"
-# suppresses any "Segmentation fault" message there. '((' could
-# trigger a bug in pdksh 5.2.14.
-for as_var in BASH_ENV ENV MAIL MAILPATH
-do eval test x\${$as_var+set} = xset \
- && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || :
-done
-PS1='$ '
-PS2='> '
-PS4='+ '
-
-# NLS nuisances.
-LC_ALL=C
-export LC_ALL
-LANGUAGE=C
-export LANGUAGE
-
-# CDPATH.
-(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
-
-# Use a proper internal environment variable to ensure we don't fall
- # into an infinite loop, continuously re-executing ourselves.
- if test x"${_as_can_reexec}" != xno && test "x$CONFIG_SHELL" != x; then
- _as_can_reexec=no; export _as_can_reexec;
- # We cannot yet assume a decent shell, so we have to provide a
-# neutralization value for shells without unset; and this also
-# works around shells that cannot unset nonexistent variables.
-# Preserve -v and -x to the replacement shell.
-BASH_ENV=/dev/null
-ENV=/dev/null
-(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-case $- in # ((((
- *v*x* | *x*v* ) as_opts=-vx ;;
- *v* ) as_opts=-v ;;
- *x* ) as_opts=-x ;;
- * ) as_opts= ;;
-esac
-exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
-# Admittedly, this is quite paranoid, since all the known shells bail
-# out after a failed `exec'.
-$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
-as_fn_exit 255
- fi
- # We don't want this to propagate to other subprocesses.
- { _as_can_reexec=; unset _as_can_reexec;}
-if test "x$CONFIG_SHELL" = x; then
- as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then :
- emulate sh
- NULLCMD=:
- # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '\${1+\"\$@\"}'='\"\$@\"'
- setopt NO_GLOB_SUBST
-else
- case \`(set -o) 2>/dev/null\` in #(
- *posix*) :
- set -o posix ;; #(
- *) :
- ;;
-esac
-fi
-"
- as_required="as_fn_return () { (exit \$1); }
-as_fn_success () { as_fn_return 0; }
-as_fn_failure () { as_fn_return 1; }
-as_fn_ret_success () { return 0; }
-as_fn_ret_failure () { return 1; }
-
-exitcode=0
-as_fn_success || { exitcode=1; echo as_fn_success failed.; }
-as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; }
-as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; }
-as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; }
-if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then :
-
-else
- exitcode=1; echo positional parameters were not saved.
-fi
-test x\$exitcode = x0 || exit 1
-test -x / || exit 1"
- as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO
- as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO
- eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" &&
- test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1
-test \$(( 1 + 1 )) = 2 || exit 1"
- if (eval "$as_required") 2>/dev/null; then :
- as_have_required=yes
-else
- as_have_required=no
-fi
- if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then :
-
-else
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-as_found=false
-for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- as_found=:
- case $as_dir in #(
- /*)
- for as_base in sh bash ksh sh5; do
- # Try only shells that exist, to save several forks.
- as_shell=$as_dir/$as_base
- if { test -f "$as_shell" || test -f "$as_shell.exe"; } &&
- { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then :
- CONFIG_SHELL=$as_shell as_have_required=yes
- if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then :
- break 2
-fi
-fi
- done;;
- esac
- as_found=false
-done
-$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } &&
- { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then :
- CONFIG_SHELL=$SHELL as_have_required=yes
-fi; }
-IFS=$as_save_IFS
-
-
- if test "x$CONFIG_SHELL" != x; then :
- export CONFIG_SHELL
- # We cannot yet assume a decent shell, so we have to provide a
-# neutralization value for shells without unset; and this also
-# works around shells that cannot unset nonexistent variables.
-# Preserve -v and -x to the replacement shell.
-BASH_ENV=/dev/null
-ENV=/dev/null
-(unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV
-case $- in # ((((
- *v*x* | *x*v* ) as_opts=-vx ;;
- *v* ) as_opts=-v ;;
- *x* ) as_opts=-x ;;
- * ) as_opts= ;;
-esac
-exec $CONFIG_SHELL $as_opts "$as_myself" ${1+"$@"}
-# Admittedly, this is quite paranoid, since all the known shells bail
-# out after a failed `exec'.
-$as_echo "$0: could not re-execute with $CONFIG_SHELL" >&2
-exit 255
-fi
-
- if test x$as_have_required = xno; then :
- $as_echo "$0: This script requires a shell more modern than all"
- $as_echo "$0: the shells that I found on your system."
- if test x${ZSH_VERSION+set} = xset ; then
- $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should"
- $as_echo "$0: be upgraded to zsh 4.3.4 or later."
- else
- $as_echo "$0: Please tell bug-autoconf at gnu.org about your system,
-$0: including any error possibly output before this
-$0: message. Then install a modern shell, or manually run
-$0: the script under such a shell if you do have one."
- fi
- exit 1
-fi
-fi
-fi
-SHELL=${CONFIG_SHELL-/bin/sh}
-export SHELL
-# Unset more variables known to interfere with behavior of common tools.
-CLICOLOR_FORCE= GREP_OPTIONS=
-unset CLICOLOR_FORCE GREP_OPTIONS
-
-## --------------------- ##
-## M4sh Shell Functions. ##
-## --------------------- ##
-# as_fn_unset VAR
-# ---------------
-# Portably unset VAR.
-as_fn_unset ()
-{
- { eval $1=; unset $1;}
-}
-as_unset=as_fn_unset
-
-# as_fn_set_status STATUS
-# -----------------------
-# Set $? to STATUS, without forking.
-as_fn_set_status ()
-{
- return $1
-} # as_fn_set_status
-
-# as_fn_exit STATUS
-# -----------------
-# Exit the shell with STATUS, even in a "trap 0" or "set -e" context.
-as_fn_exit ()
-{
- set +e
- as_fn_set_status $1
- exit $1
-} # as_fn_exit
-
-# as_fn_mkdir_p
-# -------------
-# Create "$as_dir" as a directory, including parents if necessary.
-as_fn_mkdir_p ()
-{
-
- case $as_dir in #(
- -*) as_dir=./$as_dir;;
- esac
- test -d "$as_dir" || eval $as_mkdir_p || {
- as_dirs=
- while :; do
- case $as_dir in #(
- *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'(
- *) as_qdir=$as_dir;;
- esac
- as_dirs="'$as_qdir' $as_dirs"
- as_dir=`$as_dirname -- "$as_dir" ||
-$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \
- X"$as_dir" : 'X\(//\)[^/]' \| \
- X"$as_dir" : 'X\(//\)$' \| \
- X"$as_dir" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X"$as_dir" |
- sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
- s//\1/
- q
- }
- /^X\(\/\/\)[^/].*/{
- s//\1/
- q
- }
- /^X\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
- test -d "$as_dir" && break
- done
- test -z "$as_dirs" || eval "mkdir $as_dirs"
- } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir"
-
-
-} # as_fn_mkdir_p
-
-# as_fn_executable_p FILE
-# -----------------------
-# Test if FILE is an executable regular file.
-as_fn_executable_p ()
-{
- test -f "$1" && test -x "$1"
-} # as_fn_executable_p
-# as_fn_append VAR VALUE
-# ----------------------
-# Append the text in VALUE to the end of the definition contained in VAR. Take
-# advantage of any shell optimizations that allow amortized linear growth over
-# repeated appends, instead of the typical quadratic growth present in naive
-# implementations.
-if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then :
- eval 'as_fn_append ()
- {
- eval $1+=\$2
- }'
-else
- as_fn_append ()
- {
- eval $1=\$$1\$2
- }
-fi # as_fn_append
-
-# as_fn_arith ARG...
-# ------------------
-# Perform arithmetic evaluation on the ARGs, and store the result in the
-# global $as_val. Take advantage of shells that can avoid forks. The arguments
-# must be portable across $(()) and expr.
-if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then :
- eval 'as_fn_arith ()
- {
- as_val=$(( $* ))
- }'
-else
- as_fn_arith ()
- {
- as_val=`expr "$@" || test $? -eq 1`
- }
-fi # as_fn_arith
-
-
-# as_fn_error STATUS ERROR [LINENO LOG_FD]
-# ----------------------------------------
-# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are
-# provided, also output the error to LOG_FD, referencing LINENO. Then exit the
-# script with STATUS, using 1 if that was 0.
-as_fn_error ()
-{
- as_status=$1; test $as_status -eq 0 && as_status=1
- if test "$4"; then
- as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack
- $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4
- fi
- $as_echo "$as_me: error: $2" >&2
- as_fn_exit $as_status
-} # as_fn_error
-
-if expr a : '\(a\)' >/dev/null 2>&1 &&
- test "X`expr 00001 : '.*\(...\)'`" = X001; then
- as_expr=expr
-else
- as_expr=false
-fi
-
-if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then
- as_basename=basename
-else
- as_basename=false
-fi
-
-if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then
- as_dirname=dirname
-else
- as_dirname=false
-fi
-
-as_me=`$as_basename -- "$0" ||
-$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \
- X"$0" : 'X\(//\)$' \| \
- X"$0" : 'X\(/\)' \| . 2>/dev/null ||
-$as_echo X/"$0" |
- sed '/^.*\/\([^/][^/]*\)\/*$/{
- s//\1/
- q
- }
- /^X\/\(\/\/\)$/{
- s//\1/
- q
- }
- /^X\/\(\/\).*/{
- s//\1/
- q
- }
- s/.*/./; q'`
-
-# Avoid depending upon Character Ranges.
-as_cr_letters='abcdefghijklmnopqrstuvwxyz'
-as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-as_cr_Letters=$as_cr_letters$as_cr_LETTERS
-as_cr_digits='0123456789'
-as_cr_alnum=$as_cr_Letters$as_cr_digits
-
-
- as_lineno_1=$LINENO as_lineno_1a=$LINENO
- as_lineno_2=$LINENO as_lineno_2a=$LINENO
- eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" &&
- test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || {
- # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-)
- sed -n '
- p
- /[$]LINENO/=
- ' <$as_myself |
- sed '
- s/[$]LINENO.*/&-/
- t lineno
- b
- :lineno
- N
- :loop
- s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/
- t loop
- s/-\n.*//
- ' >$as_me.lineno &&
- chmod +x "$as_me.lineno" ||
- { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; }
-
- # If we had to re-execute with $CONFIG_SHELL, we're ensured to have
- # already done that, so ensure we don't try to do so again and fall
- # in an infinite loop. This has already happened in practice.
- _as_can_reexec=no; export _as_can_reexec
- # Don't try to exec as it changes $[0], causing all sort of problems
- # (the dirname of $[0] is not the place where we might find the
- # original and so on. Autoconf is especially sensitive to this).
- . "./$as_me.lineno"
- # Exit status is that of the last command.
- exit
-}
-
-ECHO_C= ECHO_N= ECHO_T=
-case `echo -n x` in #(((((
--n*)
- case `echo 'xy\c'` in
- *c*) ECHO_T=' ';; # ECHO_T is single tab character.
- xy) ECHO_C='\c';;
- *) echo `echo ksh88 bug on AIX 6.1` > /dev/null
- ECHO_T=' ';;
- esac;;
-*)
- ECHO_N='-n';;
-esac
-
-rm -f conf$$ conf$$.exe conf$$.file
-if test -d conf$$.dir; then
- rm -f conf$$.dir/conf$$.file
-else
- rm -f conf$$.dir
- mkdir conf$$.dir 2>/dev/null
-fi
-if (echo >conf$$.file) 2>/dev/null; then
- if ln -s conf$$.file conf$$ 2>/dev/null; then
- as_ln_s='ln -s'
- # ... but there are two gotchas:
- # 1) On MSYS, both `ln -s file dir' and `ln file dir' fail.
- # 2) DJGPP < 2.04 has no symlinks; `ln -s' creates a wrapper executable.
- # In both cases, we have to default to `cp -pR'.
- ln -s conf$$.file conf$$.dir 2>/dev/null && test ! -f conf$$.exe ||
- as_ln_s='cp -pR'
- elif ln conf$$.file conf$$ 2>/dev/null; then
- as_ln_s=ln
- else
- as_ln_s='cp -pR'
- fi
-else
- as_ln_s='cp -pR'
-fi
-rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file
-rmdir conf$$.dir 2>/dev/null
-
-if mkdir -p . 2>/dev/null; then
- as_mkdir_p='mkdir -p "$as_dir"'
-else
- test -d ./-p && rmdir ./-p
- as_mkdir_p=false
-fi
-
-as_test_x='test -x'
-as_executable_p=as_fn_executable_p
-
-# Sed expression to map a string onto a valid CPP name.
-as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'"
-
-# Sed expression to map a string onto a valid variable name.
-as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'"
-
-
-test -n "$DJDIR" || exec 7<&0 </dev/null
-exec 6>&1
-
-# Name of the host.
-# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status,
-# so uname gets run too.
-ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q`
-
-#
-# Initializations.
-#
-ac_default_prefix=/usr/local
-ac_clean_files=
-ac_config_libobj_dir=.
-LIBOBJS=
-cross_compiling=no
-subdirs=
-MFLAGS=
-MAKEFLAGS=
-
-# Identity of this package.
-PACKAGE_NAME='andi'
-PACKAGE_TARNAME='andi'
-PACKAGE_VERSION='0.9.4'
-PACKAGE_STRING='andi 0.9.4'
-PACKAGE_BUGREPORT=''
-PACKAGE_URL=''
-
-# Factoring default headers for most tests.
-ac_includes_default="\
-#include <stdio.h>
-#ifdef HAVE_SYS_TYPES_H
-# include <sys/types.h>
-#endif
-#ifdef HAVE_SYS_STAT_H
-# include <sys/stat.h>
-#endif
-#ifdef STDC_HEADERS
-# include <stdlib.h>
-# include <stddef.h>
-#else
-# ifdef HAVE_STDLIB_H
-# include <stdlib.h>
-# endif
-#endif
-#ifdef HAVE_STRING_H
-# if !defined STDC_HEADERS && defined HAVE_MEMORY_H
-# include <memory.h>
-# endif
-# include <string.h>
-#endif
-#ifdef HAVE_STRINGS_H
-# include <strings.h>
-#endif
-#ifdef HAVE_INTTYPES_H
-# include <inttypes.h>
-#endif
-#ifdef HAVE_STDINT_H
-# include <stdint.h>
-#endif
-#ifdef HAVE_UNISTD_H
-# include <unistd.h>
-#endif"
-
-ac_subst_vars='am__EXEEXT_FALSE
-am__EXEEXT_TRUE
-LTLIBOBJS
-LIBOBJS
-HAVE_STRCHRNUL_FALSE
-HAVE_STRCHRNUL_TRUE
-HAVE_REALLOCARRAY_FALSE
-HAVE_REALLOCARRAY_TRUE
-GLIB_LIBS
-GLIB_CFLAGS
-PKG_CONFIG_LIBDIR
-PKG_CONFIG_PATH
-PKG_CONFIG
-BUILD_TESTS_FALSE
-BUILD_TESTS_TRUE
-BUILD_WITH_LIBDIVSUFSORT_FALSE
-BUILD_WITH_LIBDIVSUFSORT_TRUE
-HAVE_CXX11
-EGREP
-GREP
-OPENMP_CFLAGS
-OPENMP_CXXFLAGS
-ac_ct_AR
-AR
-RANLIB
-CPP
-am__fastdepCXX_FALSE
-am__fastdepCXX_TRUE
-CXXDEPMODE
-ac_ct_CXX
-CXXFLAGS
-CXX
-am__fastdepCC_FALSE
-am__fastdepCC_TRUE
-CCDEPMODE
-am__nodep
-AMDEPBACKSLASH
-AMDEP_FALSE
-AMDEP_TRUE
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-fi
-
-
- test -n "$ac_ct_AR" && break
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-
- if test "x$ac_ct_AR" = x; then
- AR="false"
- else
- case $cross_compiling:$ac_tool_warned in
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-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
-$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
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-esac
- AR=$ac_ct_AR
- fi
-fi
-
-: ${AR=ar}
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking the archiver ($AR) interface" >&5
-$as_echo_n "checking the archiver ($AR) interface... " >&6; }
-if ${am_cv_ar_interface+:} false; then :
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-else
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- am_cv_ar_interface=ar
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-int some_variable = 0;
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- am_ar_try='$AR cru libconftest.a conftest.$ac_objext >&5'
- { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$am_ar_try\""; } >&5
- (eval $am_ar_try) 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }
- if test "$ac_status" -eq 0; then
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- else
- am_ar_try='$AR -NOLOGO -OUT:conftest.lib conftest.$ac_objext >&5'
- { { eval echo "\"\$as_me\":${as_lineno-$LINENO}: \"$am_ar_try\""; } >&5
- (eval $am_ar_try) 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }
- if test "$ac_status" -eq 0; then
- am_cv_ar_interface=lib
- else
- am_cv_ar_interface=unknown
- fi
- fi
- rm -f conftest.lib libconftest.a
-
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_ar_interface" >&5
-$as_echo "$am_cv_ar_interface" >&6; }
-
-case $am_cv_ar_interface in
-ar)
- ;;
-lib)
- # Microsoft lib, so override with the ar-lib wrapper script.
- # FIXME: It is wrong to rewrite AR.
- # But if we don't then we get into trouble of one sort or another.
- # A longer-term fix would be to have automake use am__AR in this case,
- # and then we could set am__AR="$am_aux_dir/ar-lib \$(AR)" or something
- # similar.
- AR="$am_aux_dir/ar-lib $AR"
- ;;
-unknown)
- as_fn_error $? "could not determine $AR interface" "$LINENO" 5
- ;;
-esac
-
-
-# Make sure, also the C++ programs are compiled with OpenMP
-ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
-
-
-
- OPENMP_CXXFLAGS=
- # Check whether --enable-openmp was given.
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- enableval=$enable_openmp;
-fi
-
- if test "$enable_openmp" != no; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CXX option to support OpenMP" >&5
-$as_echo_n "checking for $CXX option to support OpenMP... " >&6; }
-if ${ac_cv_prog_cxx_openmp+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-#ifndef _OPENMP
- choke me
-#endif
-#include <omp.h>
-int main () { return omp_get_num_threads (); }
-
-_ACEOF
-if ac_fn_cxx_try_link "$LINENO"; then :
- ac_cv_prog_cxx_openmp='none needed'
-else
- ac_cv_prog_cxx_openmp='unsupported'
- for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp -homp \
- -Popenmp --openmp; do
- ac_save_CXXFLAGS=$CXXFLAGS
- CXXFLAGS="$CXXFLAGS $ac_option"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-#ifndef _OPENMP
- choke me
-#endif
-#include <omp.h>
-int main () { return omp_get_num_threads (); }
-
-_ACEOF
-if ac_fn_cxx_try_link "$LINENO"; then :
- ac_cv_prog_cxx_openmp=$ac_option
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
- CXXFLAGS=$ac_save_CXXFLAGS
- if test "$ac_cv_prog_cxx_openmp" != unsupported; then
- break
- fi
- done
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_openmp" >&5
-$as_echo "$ac_cv_prog_cxx_openmp" >&6; }
- case $ac_cv_prog_cxx_openmp in #(
- "none needed" | unsupported)
- ;; #(
- *)
- OPENMP_CXXFLAGS=$ac_cv_prog_cxx_openmp ;;
- esac
- fi
-
-
-
-# Execute all tests using C
-ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for cos in -lm" >&5
-$as_echo_n "checking for cos in -lm... " >&6; }
-if ${ac_cv_lib_m_cos+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-lm $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char cos ();
-int
-main ()
-{
-return cos ();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_lib_m_cos=yes
-else
- ac_cv_lib_m_cos=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_cos" >&5
-$as_echo "$ac_cv_lib_m_cos" >&6; }
-if test "x$ac_cv_lib_m_cos" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_LIBM 1
-_ACEOF
-
- LIBS="-lm $LIBS"
-
-fi
-
-
- OPENMP_CFLAGS=
- # Check whether --enable-openmp was given.
-if test "${enable_openmp+set}" = set; then :
- enableval=$enable_openmp;
-fi
-
- if test "$enable_openmp" != no; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5
-$as_echo_n "checking for $CC option to support OpenMP... " >&6; }
-if ${ac_cv_prog_c_openmp+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-#ifndef _OPENMP
- choke me
-#endif
-#include <omp.h>
-int main () { return omp_get_num_threads (); }
-
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_prog_c_openmp='none needed'
-else
- ac_cv_prog_c_openmp='unsupported'
- for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp -homp \
- -Popenmp --openmp; do
- ac_save_CFLAGS=$CFLAGS
- CFLAGS="$CFLAGS $ac_option"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-#ifndef _OPENMP
- choke me
-#endif
-#include <omp.h>
-int main () { return omp_get_num_threads (); }
-
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_prog_c_openmp=$ac_option
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
- CFLAGS=$ac_save_CFLAGS
- if test "$ac_cv_prog_c_openmp" != unsupported; then
- break
- fi
- done
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_c_openmp" >&5
-$as_echo "$ac_cv_prog_c_openmp" >&6; }
- case $ac_cv_prog_c_openmp in #(
- "none needed" | unsupported)
- ;; #(
- *)
- OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;;
- esac
- fi
-
-
-
-# By default try to build with libdivsufsort.
-
-# Check whether --with-libdivsufsort was given.
-if test "${with_libdivsufsort+set}" = set; then :
- withval=$with_libdivsufsort;
-fi
-
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5
-$as_echo_n "checking for grep that handles long lines and -e... " >&6; }
-if ${ac_cv_path_GREP+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if test -z "$GREP"; then
- ac_path_GREP_found=false
- # Loop through the user's path and test for each of PROGNAME-LIST
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_prog in grep ggrep; do
- for ac_exec_ext in '' $ac_executable_extensions; do
- ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext"
- as_fn_executable_p "$ac_path_GREP" || continue
-# Check for GNU ac_path_GREP and select it if it is found.
- # Check for GNU $ac_path_GREP
-case `"$ac_path_GREP" --version 2>&1` in
-*GNU*)
- ac_cv_path_GREP="$ac_path_GREP" ac_path_GREP_found=:;;
-*)
- ac_count=0
- $as_echo_n 0123456789 >"conftest.in"
- while :
- do
- cat "conftest.in" "conftest.in" >"conftest.tmp"
- mv "conftest.tmp" "conftest.in"
- cp "conftest.in" "conftest.nl"
- $as_echo 'GREP' >> "conftest.nl"
- "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break
- diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
- as_fn_arith $ac_count + 1 && ac_count=$as_val
- if test $ac_count -gt ${ac_path_GREP_max-0}; then
- # Best one so far, save it but keep looking for a better one
- ac_cv_path_GREP="$ac_path_GREP"
- ac_path_GREP_max=$ac_count
- fi
- # 10*(2^10) chars as input seems more than enough
- test $ac_count -gt 10 && break
- done
- rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
-esac
-
- $ac_path_GREP_found && break 3
- done
- done
- done
-IFS=$as_save_IFS
- if test -z "$ac_cv_path_GREP"; then
- as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
- fi
-else
- ac_cv_path_GREP=$GREP
-fi
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5
-$as_echo "$ac_cv_path_GREP" >&6; }
- GREP="$ac_cv_path_GREP"
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5
-$as_echo_n "checking for egrep... " >&6; }
-if ${ac_cv_path_EGREP+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- if echo a | $GREP -E '(a|b)' >/dev/null 2>&1
- then ac_cv_path_EGREP="$GREP -E"
- else
- if test -z "$EGREP"; then
- ac_path_EGREP_found=false
- # Loop through the user's path and test for each of PROGNAME-LIST
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_prog in egrep; do
- for ac_exec_ext in '' $ac_executable_extensions; do
- ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext"
- as_fn_executable_p "$ac_path_EGREP" || continue
-# Check for GNU ac_path_EGREP and select it if it is found.
- # Check for GNU $ac_path_EGREP
-case `"$ac_path_EGREP" --version 2>&1` in
-*GNU*)
- ac_cv_path_EGREP="$ac_path_EGREP" ac_path_EGREP_found=:;;
-*)
- ac_count=0
- $as_echo_n 0123456789 >"conftest.in"
- while :
- do
- cat "conftest.in" "conftest.in" >"conftest.tmp"
- mv "conftest.tmp" "conftest.in"
- cp "conftest.in" "conftest.nl"
- $as_echo 'EGREP' >> "conftest.nl"
- "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break
- diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break
- as_fn_arith $ac_count + 1 && ac_count=$as_val
- if test $ac_count -gt ${ac_path_EGREP_max-0}; then
- # Best one so far, save it but keep looking for a better one
- ac_cv_path_EGREP="$ac_path_EGREP"
- ac_path_EGREP_max=$ac_count
- fi
- # 10*(2^10) chars as input seems more than enough
- test $ac_count -gt 10 && break
- done
- rm -f conftest.in conftest.tmp conftest.nl conftest.out;;
-esac
-
- $ac_path_EGREP_found && break 3
- done
- done
- done
-IFS=$as_save_IFS
- if test -z "$ac_cv_path_EGREP"; then
- as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5
- fi
-else
- ac_cv_path_EGREP=$EGREP
-fi
-
- fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5
-$as_echo "$ac_cv_path_EGREP" >&6; }
- EGREP="$ac_cv_path_EGREP"
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5
-$as_echo_n "checking for ANSI C header files... " >&6; }
-if ${ac_cv_header_stdc+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <stdlib.h>
-#include <stdarg.h>
-#include <string.h>
-#include <float.h>
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_header_stdc=yes
-else
- ac_cv_header_stdc=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-
-if test $ac_cv_header_stdc = yes; then
- # SunOS 4.x string.h does not declare mem*, contrary to ANSI.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <string.h>
-
-_ACEOF
-if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "memchr" >/dev/null 2>&1; then :
-
-else
- ac_cv_header_stdc=no
-fi
-rm -f conftest*
-
-fi
-
-if test $ac_cv_header_stdc = yes; then
- # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <stdlib.h>
-
-_ACEOF
-if (eval "$ac_cpp conftest.$ac_ext") 2>&5 |
- $EGREP "free" >/dev/null 2>&1; then :
-
-else
- ac_cv_header_stdc=no
-fi
-rm -f conftest*
-
-fi
-
-if test $ac_cv_header_stdc = yes; then
- # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi.
- if test "$cross_compiling" = yes; then :
- :
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#include <ctype.h>
-#include <stdlib.h>
-#if ((' ' & 0x0FF) == 0x020)
-# define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
-# define TOUPPER(c) (ISLOWER(c) ? 'A' + ((c) - 'a') : (c))
-#else
-# define ISLOWER(c) \
- (('a' <= (c) && (c) <= 'i') \
- || ('j' <= (c) && (c) <= 'r') \
- || ('s' <= (c) && (c) <= 'z'))
-# define TOUPPER(c) (ISLOWER(c) ? ((c) | 0x40) : (c))
-#endif
-
-#define XOR(e, f) (((e) && !(f)) || (!(e) && (f)))
-int
-main ()
-{
- int i;
- for (i = 0; i < 256; i++)
- if (XOR (islower (i), ISLOWER (i))
- || toupper (i) != TOUPPER (i))
- return 2;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_run "$LINENO"; then :
-
-else
- ac_cv_header_stdc=no
-fi
-rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
- conftest.$ac_objext conftest.beam conftest.$ac_ext
-fi
-
-fi
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5
-$as_echo "$ac_cv_header_stdc" >&6; }
-if test $ac_cv_header_stdc = yes; then
-
-$as_echo "#define STDC_HEADERS 1" >>confdefs.h
-
-fi
-
-# On IRIX 5.3, sys/types and inttypes.h are conflicting.
-for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \
- inttypes.h stdint.h unistd.h
-do :
- as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default
-"
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-
-done
-
-
-if test "x$with_libdivsufsort" != "xno"; then :
-
- for ac_header in divsufsort.h
-do :
- ac_fn_c_check_header_mongrel "$LINENO" "divsufsort.h" "ac_cv_header_divsufsort_h" "$ac_includes_default"
-if test "x$ac_cv_header_divsufsort_h" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_DIVSUFSORT_H 1
-_ACEOF
- have_libdivsufsort=yes
-else
- have_libdivsufsort=no
-fi
-
-done
-
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for divsufsort in -ldivsufsort" >&5
-$as_echo_n "checking for divsufsort in -ldivsufsort... " >&6; }
-if ${ac_cv_lib_divsufsort_divsufsort+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_check_lib_save_LIBS=$LIBS
-LIBS="-ldivsufsort $LIBS"
-cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-/* Override any GCC internal prototype to avoid an error.
- Use char because int might match the return type of a GCC
- builtin and then its argument prototype would still apply. */
-#ifdef __cplusplus
-extern "C"
-#endif
-char divsufsort ();
-int
-main ()
-{
-return divsufsort ();
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_link "$LINENO"; then :
- ac_cv_lib_divsufsort_divsufsort=yes
-else
- ac_cv_lib_divsufsort_divsufsort=no
-fi
-rm -f core conftest.err conftest.$ac_objext \
- conftest$ac_exeext conftest.$ac_ext
-LIBS=$ac_check_lib_save_LIBS
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_divsufsort_divsufsort" >&5
-$as_echo "$ac_cv_lib_divsufsort_divsufsort" >&6; }
-if test "x$ac_cv_lib_divsufsort_divsufsort" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_LIBDIVSUFSORT 1
-_ACEOF
-
- LIBS="-ldivsufsort $LIBS"
-
-else
- have_libdivsufsort=no
-fi
-
-
-else
-
- have_libdivsufsort=no
- # psufsort needs C++11
- ax_cxx_compile_cxx11_required=true
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
- ac_success=no
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features by default" >&5
-$as_echo_n "checking whether $CXX supports C++11 features by default... " >&6; }
-if ${ax_cv_cxx_compile_cxx11+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- template <typename T>
- struct check
- {
- static_assert(sizeof(int) <= sizeof(T), "not big enough");
- };
-
- struct Base {
- virtual void f() {}
- };
- struct Child : public Base {
- virtual void f() override {}
- };
-
- typedef check<check<bool>> right_angle_brackets;
-
- int a;
- decltype(a) b;
-
- typedef check<int> check_type;
- check_type c;
- check_type&& cr = static_cast<check_type&&>(c);
-
- auto d = a;
- auto l = [](){};
-
- // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
- // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this
- namespace test_template_alias_sfinae {
- struct foo {};
-
- template<typename T>
- using member = typename T::member_type;
-
- template<typename T>
- void func(...) {}
-
- template<typename T>
- void func(member<T>*) {}
-
- void test() {
- func<foo>(0);
- }
- }
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- ax_cv_cxx_compile_cxx11=yes
-else
- ax_cv_cxx_compile_cxx11=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_cxx_compile_cxx11" >&5
-$as_echo "$ax_cv_cxx_compile_cxx11" >&6; }
- if test x$ax_cv_cxx_compile_cxx11 = xyes; then
- ac_success=yes
- fi
-
- if test x$ac_success = xno; then
- for switch in -std=gnu++11 -std=gnu++0x; do
- cachevar=`$as_echo "ax_cv_cxx_compile_cxx11_$switch" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features with $switch" >&5
-$as_echo_n "checking whether $CXX supports C++11 features with $switch... " >&6; }
-if eval \${$cachevar+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_save_CXXFLAGS="$CXXFLAGS"
- CXXFLAGS="$CXXFLAGS $switch"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- template <typename T>
- struct check
- {
- static_assert(sizeof(int) <= sizeof(T), "not big enough");
- };
-
- struct Base {
- virtual void f() {}
- };
- struct Child : public Base {
- virtual void f() override {}
- };
-
- typedef check<check<bool>> right_angle_brackets;
-
- int a;
- decltype(a) b;
-
- typedef check<int> check_type;
- check_type c;
- check_type&& cr = static_cast<check_type&&>(c);
-
- auto d = a;
- auto l = [](){};
-
- // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
- // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this
- namespace test_template_alias_sfinae {
- struct foo {};
-
- template<typename T>
- using member = typename T::member_type;
-
- template<typename T>
- void func(...) {}
-
- template<typename T>
- void func(member<T>*) {}
-
- void test() {
- func<foo>(0);
- }
- }
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- eval $cachevar=yes
-else
- eval $cachevar=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CXXFLAGS="$ac_save_CXXFLAGS"
-fi
-eval ac_res=\$$cachevar
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
- if eval test x\$$cachevar = xyes; then
- CXXFLAGS="$CXXFLAGS $switch"
- ac_success=yes
- break
- fi
- done
- fi
-
- if test x$ac_success = xno; then
- for switch in -std=c++11 -std=c++0x; do
- cachevar=`$as_echo "ax_cv_cxx_compile_cxx11_$switch" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features with $switch" >&5
-$as_echo_n "checking whether $CXX supports C++11 features with $switch... " >&6; }
-if eval \${$cachevar+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_save_CXXFLAGS="$CXXFLAGS"
- CXXFLAGS="$CXXFLAGS $switch"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- template <typename T>
- struct check
- {
- static_assert(sizeof(int) <= sizeof(T), "not big enough");
- };
-
- struct Base {
- virtual void f() {}
- };
- struct Child : public Base {
- virtual void f() override {}
- };
-
- typedef check<check<bool>> right_angle_brackets;
-
- int a;
- decltype(a) b;
-
- typedef check<int> check_type;
- check_type c;
- check_type&& cr = static_cast<check_type&&>(c);
-
- auto d = a;
- auto l = [](){};
-
- // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
- // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this
- namespace test_template_alias_sfinae {
- struct foo {};
-
- template<typename T>
- using member = typename T::member_type;
-
- template<typename T>
- void func(...) {}
-
- template<typename T>
- void func(member<T>*) {}
-
- void test() {
- func<foo>(0);
- }
- }
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- eval $cachevar=yes
-else
- eval $cachevar=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CXXFLAGS="$ac_save_CXXFLAGS"
-fi
-eval ac_res=\$$cachevar
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
- if eval test x\$$cachevar = xyes; then
- CXXFLAGS="$CXXFLAGS $switch"
- ac_success=yes
- break
- fi
- done
- fi
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- if test x$ax_cxx_compile_cxx11_required = xtrue; then
- if test x$ac_success = xno; then
- as_fn_error $? "*** A compiler with support for C++11 language features is required." "$LINENO" 5
- fi
- else
- if test x$ac_success = xno; then
- HAVE_CXX11=0
- { $as_echo "$as_me:${as_lineno-$LINENO}: No compiler with C++11 support was found" >&5
-$as_echo "$as_me: No compiler with C++11 support was found" >&6;}
- else
- HAVE_CXX11=1
-
-$as_echo "#define HAVE_CXX11 1" >>confdefs.h
-
- fi
-
-
- fi
-
-
-
-fi
-
-if test "x$have_libdivsufsort" = "xno"; then :
- if test "x$with_libdivsufsort" != "xno"; then :
- as_fn_error $? "Configuration for libdivsufsort failed. Either install libdivsufsort, or use our replacement, psufsort, instead.
- ./configure --without-libdivsufsort
-The latter may result in longer runtimes." "$LINENO" 5
-
-fi
-
-fi
-
- if test "x${with_libdivsufsort}" != "xno"; then
- BUILD_WITH_LIBDIVSUFSORT_TRUE=
- BUILD_WITH_LIBDIVSUFSORT_FALSE='#'
-else
- BUILD_WITH_LIBDIVSUFSORT_TRUE='#'
- BUILD_WITH_LIBDIVSUFSORT_FALSE=
-fi
-
-
-# The unit tests require GLIB2. So by default do not build the test.
-# If enabled, check for glib.
-
-# Check whether --enable-unit-tests was given.
-if test "${enable_unit_tests+set}" = set; then :
- enableval=$enable_unit_tests; try_unit_tests=${enableval}
-else
- try_unit_tests=no
-
-fi
-
-
- if test "x${try_unit_tests}" = xyes; then
- BUILD_TESTS_TRUE=
- BUILD_TESTS_FALSE='#'
-else
- BUILD_TESTS_TRUE='#'
- BUILD_TESTS_FALSE=
-fi
-
-
-if test "x${try_unit_tests}" = xyes; then
-
- have_glib=yes
-
-
-
-
-
-
-
-if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then
- if test -n "$ac_tool_prefix"; then
- # Extract the first word of "${ac_tool_prefix}pkg-config", so it can be a program name with args.
-set dummy ${ac_tool_prefix}pkg-config; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_path_PKG_CONFIG+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- case $PKG_CONFIG in
- [\\/]* | ?:[\\/]*)
- ac_cv_path_PKG_CONFIG="$PKG_CONFIG" # Let the user override the test with a path.
- ;;
- *)
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_path_PKG_CONFIG="$as_dir/$ac_word$ac_exec_ext"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
- ;;
-esac
-fi
-PKG_CONFIG=$ac_cv_path_PKG_CONFIG
-if test -n "$PKG_CONFIG"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $PKG_CONFIG" >&5
-$as_echo "$PKG_CONFIG" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
-
-fi
-if test -z "$ac_cv_path_PKG_CONFIG"; then
- ac_pt_PKG_CONFIG=$PKG_CONFIG
- # Extract the first word of "pkg-config", so it can be a program name with args.
-set dummy pkg-config; ac_word=$2
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
-$as_echo_n "checking for $ac_word... " >&6; }
-if ${ac_cv_path_ac_pt_PKG_CONFIG+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- case $ac_pt_PKG_CONFIG in
- [\\/]* | ?:[\\/]*)
- ac_cv_path_ac_pt_PKG_CONFIG="$ac_pt_PKG_CONFIG" # Let the user override the test with a path.
- ;;
- *)
- as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- for ac_exec_ext in '' $ac_executable_extensions; do
- if as_fn_executable_p "$as_dir/$ac_word$ac_exec_ext"; then
- ac_cv_path_ac_pt_PKG_CONFIG="$as_dir/$ac_word$ac_exec_ext"
- $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5
- break 2
- fi
-done
- done
-IFS=$as_save_IFS
-
- ;;
-esac
-fi
-ac_pt_PKG_CONFIG=$ac_cv_path_ac_pt_PKG_CONFIG
-if test -n "$ac_pt_PKG_CONFIG"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_pt_PKG_CONFIG" >&5
-$as_echo "$ac_pt_PKG_CONFIG" >&6; }
-else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-fi
-
- if test "x$ac_pt_PKG_CONFIG" = x; then
- PKG_CONFIG=""
- else
- case $cross_compiling:$ac_tool_warned in
-yes:)
-{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5
-$as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;}
-ac_tool_warned=yes ;;
-esac
- PKG_CONFIG=$ac_pt_PKG_CONFIG
- fi
-else
- PKG_CONFIG="$ac_cv_path_PKG_CONFIG"
-fi
-
-fi
-if test -n "$PKG_CONFIG"; then
- _pkg_min_version=0.9.0
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking pkg-config is at least version $_pkg_min_version" >&5
-$as_echo_n "checking pkg-config is at least version $_pkg_min_version... " >&6; }
- if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
- else
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
- PKG_CONFIG=""
- fi
-fi
-
-pkg_failed=no
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GLIB" >&5
-$as_echo_n "checking for GLIB... " >&6; }
-
-if test -n "$GLIB_CFLAGS"; then
- pkg_cv_GLIB_CFLAGS="$GLIB_CFLAGS"
- elif test -n "$PKG_CONFIG"; then
- if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"glib-2.0\""; } >&5
- ($PKG_CONFIG --exists --print-errors "glib-2.0") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; then
- pkg_cv_GLIB_CFLAGS=`$PKG_CONFIG --cflags "glib-2.0" 2>/dev/null`
- test "x$?" != "x0" && pkg_failed=yes
-else
- pkg_failed=yes
-fi
- else
- pkg_failed=untried
-fi
-if test -n "$GLIB_LIBS"; then
- pkg_cv_GLIB_LIBS="$GLIB_LIBS"
- elif test -n "$PKG_CONFIG"; then
- if test -n "$PKG_CONFIG" && \
- { { $as_echo "$as_me:${as_lineno-$LINENO}: \$PKG_CONFIG --exists --print-errors \"glib-2.0\""; } >&5
- ($PKG_CONFIG --exists --print-errors "glib-2.0") 2>&5
- ac_status=$?
- $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5
- test $ac_status = 0; }; then
- pkg_cv_GLIB_LIBS=`$PKG_CONFIG --libs "glib-2.0" 2>/dev/null`
- test "x$?" != "x0" && pkg_failed=yes
-else
- pkg_failed=yes
-fi
- else
- pkg_failed=untried
-fi
-
-
-
-if test $pkg_failed = yes; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
-
-if $PKG_CONFIG --atleast-pkgconfig-version 0.20; then
- _pkg_short_errors_supported=yes
-else
- _pkg_short_errors_supported=no
-fi
- if test $_pkg_short_errors_supported = yes; then
- GLIB_PKG_ERRORS=`$PKG_CONFIG --short-errors --print-errors --cflags --libs "glib-2.0" 2>&1`
- else
- GLIB_PKG_ERRORS=`$PKG_CONFIG --print-errors --cflags --libs "glib-2.0" 2>&1`
- fi
- # Put the nasty error message in config.log where it belongs
- echo "$GLIB_PKG_ERRORS" >&5
-
- have_glib=no
-elif test $pkg_failed = untried; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
-$as_echo "no" >&6; }
- have_glib=no
-else
- GLIB_CFLAGS=$pkg_cv_GLIB_CFLAGS
- GLIB_LIBS=$pkg_cv_GLIB_LIBS
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
-$as_echo "yes" >&6; }
-
-fi
-
- if test "x${have_glib}" = xno; then
- as_fn_error $? "Missing Glib 2. Either install it or build without unit tests." "$LINENO" 5
- fi
-
- ax_cxx_compile_cxx11_required=true
- ac_ext=cpp
-ac_cpp='$CXXCPP $CPPFLAGS'
-ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
- ac_success=no
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features by default" >&5
-$as_echo_n "checking whether $CXX supports C++11 features by default... " >&6; }
-if ${ax_cv_cxx_compile_cxx11+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- template <typename T>
- struct check
- {
- static_assert(sizeof(int) <= sizeof(T), "not big enough");
- };
-
- struct Base {
- virtual void f() {}
- };
- struct Child : public Base {
- virtual void f() override {}
- };
-
- typedef check<check<bool>> right_angle_brackets;
-
- int a;
- decltype(a) b;
-
- typedef check<int> check_type;
- check_type c;
- check_type&& cr = static_cast<check_type&&>(c);
-
- auto d = a;
- auto l = [](){};
-
- // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
- // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this
- namespace test_template_alias_sfinae {
- struct foo {};
-
- template<typename T>
- using member = typename T::member_type;
-
- template<typename T>
- void func(...) {}
-
- template<typename T>
- void func(member<T>*) {}
-
- void test() {
- func<foo>(0);
- }
- }
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- ax_cv_cxx_compile_cxx11=yes
-else
- ax_cv_cxx_compile_cxx11=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_cxx_compile_cxx11" >&5
-$as_echo "$ax_cv_cxx_compile_cxx11" >&6; }
- if test x$ax_cv_cxx_compile_cxx11 = xyes; then
- ac_success=yes
- fi
-
- if test x$ac_success = xno; then
- for switch in -std=gnu++11 -std=gnu++0x; do
- cachevar=`$as_echo "ax_cv_cxx_compile_cxx11_$switch" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features with $switch" >&5
-$as_echo_n "checking whether $CXX supports C++11 features with $switch... " >&6; }
-if eval \${$cachevar+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_save_CXXFLAGS="$CXXFLAGS"
- CXXFLAGS="$CXXFLAGS $switch"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- template <typename T>
- struct check
- {
- static_assert(sizeof(int) <= sizeof(T), "not big enough");
- };
-
- struct Base {
- virtual void f() {}
- };
- struct Child : public Base {
- virtual void f() override {}
- };
-
- typedef check<check<bool>> right_angle_brackets;
-
- int a;
- decltype(a) b;
-
- typedef check<int> check_type;
- check_type c;
- check_type&& cr = static_cast<check_type&&>(c);
-
- auto d = a;
- auto l = [](){};
-
- // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
- // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this
- namespace test_template_alias_sfinae {
- struct foo {};
-
- template<typename T>
- using member = typename T::member_type;
-
- template<typename T>
- void func(...) {}
-
- template<typename T>
- void func(member<T>*) {}
-
- void test() {
- func<foo>(0);
- }
- }
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- eval $cachevar=yes
-else
- eval $cachevar=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CXXFLAGS="$ac_save_CXXFLAGS"
-fi
-eval ac_res=\$$cachevar
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
- if eval test x\$$cachevar = xyes; then
- CXXFLAGS="$CXXFLAGS $switch"
- ac_success=yes
- break
- fi
- done
- fi
-
- if test x$ac_success = xno; then
- for switch in -std=c++11 -std=c++0x; do
- cachevar=`$as_echo "ax_cv_cxx_compile_cxx11_$switch" | $as_tr_sh`
- { $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX supports C++11 features with $switch" >&5
-$as_echo_n "checking whether $CXX supports C++11 features with $switch... " >&6; }
-if eval \${$cachevar+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_save_CXXFLAGS="$CXXFLAGS"
- CXXFLAGS="$CXXFLAGS $switch"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- template <typename T>
- struct check
- {
- static_assert(sizeof(int) <= sizeof(T), "not big enough");
- };
-
- struct Base {
- virtual void f() {}
- };
- struct Child : public Base {
- virtual void f() override {}
- };
-
- typedef check<check<bool>> right_angle_brackets;
-
- int a;
- decltype(a) b;
-
- typedef check<int> check_type;
- check_type c;
- check_type&& cr = static_cast<check_type&&>(c);
-
- auto d = a;
- auto l = [](){};
-
- // http://stackoverflow.com/questions/13728184/template-aliases-and-sfinae
- // Clang 3.1 fails with headers of libstd++ 4.8.3 when using std::function because of this
- namespace test_template_alias_sfinae {
- struct foo {};
-
- template<typename T>
- using member = typename T::member_type;
-
- template<typename T>
- void func(...) {}
-
- template<typename T>
- void func(member<T>*) {}
-
- void test() {
- func<foo>(0);
- }
- }
-
-_ACEOF
-if ac_fn_cxx_try_compile "$LINENO"; then :
- eval $cachevar=yes
-else
- eval $cachevar=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CXXFLAGS="$ac_save_CXXFLAGS"
-fi
-eval ac_res=\$$cachevar
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
-$as_echo "$ac_res" >&6; }
- if eval test x\$$cachevar = xyes; then
- CXXFLAGS="$CXXFLAGS $switch"
- ac_success=yes
- break
- fi
- done
- fi
- ac_ext=c
-ac_cpp='$CPP $CPPFLAGS'
-ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
-ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
-ac_compiler_gnu=$ac_cv_c_compiler_gnu
-
- if test x$ax_cxx_compile_cxx11_required = xtrue; then
- if test x$ac_success = xno; then
- as_fn_error $? "*** A compiler with support for C++11 language features is required." "$LINENO" 5
- fi
- else
- if test x$ac_success = xno; then
- HAVE_CXX11=0
- { $as_echo "$as_me:${as_lineno-$LINENO}: No compiler with C++11 support was found" >&5
-$as_echo "$as_me: No compiler with C++11 support was found" >&6;}
- else
- HAVE_CXX11=1
-
-$as_echo "#define HAVE_CXX11 1" >>confdefs.h
-
- fi
-
-
- fi
-
-fi
-
-# Check for various headers including those used by libdivsufsort.
-for ac_header in limits.h stdlib.h string.h unistd.h stdint.h inttypes.h err.h errno.h fcntl.h
-do :
- as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh`
-ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default"
-if eval test \"x\$"$as_ac_Header"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-
-done
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5
-$as_echo_n "checking for inline... " >&6; }
-if ${ac_cv_c_inline+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- ac_cv_c_inline=no
-for ac_kw in inline __inline__ __inline; do
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-#ifndef __cplusplus
-typedef int foo_t;
-static $ac_kw foo_t static_foo () {return 0; }
-$ac_kw foo_t foo () {return 0; }
-#endif
-
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_c_inline=$ac_kw
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- test "$ac_cv_c_inline" != no && break
-done
-
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5
-$as_echo "$ac_cv_c_inline" >&6; }
-
-case $ac_cv_c_inline in
- inline | yes) ;;
- *)
- case $ac_cv_c_inline in
- no) ac_val=;;
- *) ac_val=$ac_cv_c_inline;;
- esac
- cat >>confdefs.h <<_ACEOF
-#ifndef __cplusplus
-#define inline $ac_val
-#endif
-_ACEOF
- ;;
-esac
-
-ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default"
-if test "x$ac_cv_type_size_t" = xyes; then :
-
-else
-
-cat >>confdefs.h <<_ACEOF
-#define size_t unsigned int
-_ACEOF
-
-fi
-
-ac_fn_c_check_type "$LINENO" "ssize_t" "ac_cv_type_ssize_t" "$ac_includes_default"
-if test "x$ac_cv_type_ssize_t" = xyes; then :
-
-else
-
-cat >>confdefs.h <<_ACEOF
-#define ssize_t int
-_ACEOF
-
-fi
-
-ac_fn_c_find_intX_t "$LINENO" "32" "ac_cv_c_int32_t"
-case $ac_cv_c_int32_t in #(
- no|yes) ;; #(
- *)
-
-cat >>confdefs.h <<_ACEOF
-#define int32_t $ac_cv_c_int32_t
-_ACEOF
-;;
-esac
-
-ac_fn_c_find_uintX_t "$LINENO" "8" "ac_cv_c_uint8_t"
-case $ac_cv_c_uint8_t in #(
- no|yes) ;; #(
- *)
-
-$as_echo "#define _UINT8_T 1" >>confdefs.h
-
-
-cat >>confdefs.h <<_ACEOF
-#define uint8_t $ac_cv_c_uint8_t
-_ACEOF
-;;
- esac
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for stdbool.h that conforms to C99" >&5
-$as_echo_n "checking for stdbool.h that conforms to C99... " >&6; }
-if ${ac_cv_header_stdbool_h+:} false; then :
- $as_echo_n "(cached) " >&6
-else
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
- #include <stdbool.h>
- #ifndef bool
- "error: bool is not defined"
- #endif
- #ifndef false
- "error: false is not defined"
- #endif
- #if false
- "error: false is not 0"
- #endif
- #ifndef true
- "error: true is not defined"
- #endif
- #if true != 1
- "error: true is not 1"
- #endif
- #ifndef __bool_true_false_are_defined
- "error: __bool_true_false_are_defined is not defined"
- #endif
-
- struct s { _Bool s: 1; _Bool t; } s;
-
- char a[true == 1 ? 1 : -1];
- char b[false == 0 ? 1 : -1];
- char c[__bool_true_false_are_defined == 1 ? 1 : -1];
- char d[(bool) 0.5 == true ? 1 : -1];
- /* See body of main program for 'e'. */
- char f[(_Bool) 0.0 == false ? 1 : -1];
- char g[true];
- char h[sizeof (_Bool)];
- char i[sizeof s.t];
- enum { j = false, k = true, l = false * true, m = true * 256 };
- /* The following fails for
- HP aC++/ANSI C B3910B A.05.55 [Dec 04 2003]. */
- _Bool n[m];
- char o[sizeof n == m * sizeof n[0] ? 1 : -1];
- char p[-1 - (_Bool) 0 < 0 && -1 - (bool) 0 < 0 ? 1 : -1];
- /* Catch a bug in an HP-UX C compiler. See
- http://gcc.gnu.org/ml/gcc-patches/2003-12/msg02303.html
- http://lists.gnu.org/archive/html/bug-coreutils/2005-11/msg00161.html
- */
- _Bool q = true;
- _Bool *pq = &q;
-
-int
-main ()
-{
-
- bool e = &s;
- *pq |= q;
- *pq |= ! q;
- /* Refer to every declared value, to avoid compiler optimizations. */
- return (!a + !b + !c + !d + !e + !f + !g + !h + !i + !!j + !k + !!l
- + !m + !n + !o + !p + !q + !pq);
-
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- ac_cv_header_stdbool_h=yes
-else
- ac_cv_header_stdbool_h=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdbool_h" >&5
-$as_echo "$ac_cv_header_stdbool_h" >&6; }
- ac_fn_c_check_type "$LINENO" "_Bool" "ac_cv_type__Bool" "$ac_includes_default"
-if test "x$ac_cv_type__Bool" = xyes; then :
-
-cat >>confdefs.h <<_ACEOF
-#define HAVE__BOOL 1
-_ACEOF
-
-
-fi
-
-
-if test $ac_cv_header_stdbool_h = yes; then
-
-$as_echo "#define HAVE_STDBOOL_H 1" >>confdefs.h
-
-fi
-
-
-# Until someone convinces me otherwise, I will deactivate the macros
-# AC_FUNC_MALLOC and AC_FUNC_REALLOC. They only check if `malloc(0)` retuns a
-# non-null pointer. This breaks the build on systems using uClibc, including
-# my laptop.
-# As requesting zero bytes is not useful, and implementation-defined behaviour,
-# I should be avoided in the first place. Thus I really don't need these checks.
-
-for ac_func in floor pow sqrt strdup strerror
-do :
- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-done
-
-for ac_func in strndup
-do :
- ac_fn_c_check_func "$LINENO" "strndup" "ac_cv_func_strndup"
-if test "x$ac_cv_func_strndup" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_STRNDUP 1
-_ACEOF
-
-fi
-done
-
-for ac_func in strchr strrchr strchrnul
-do :
- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-done
-
-for ac_func in strtoul strtod
-do :
- as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh`
-ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var"
-if eval test \"x\$"$as_ac_var"\" = x"yes"; then :
- cat >>confdefs.h <<_ACEOF
-#define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1
-_ACEOF
-
-fi
-done
-
-for ac_func in reallocarray
-do :
- ac_fn_c_check_func "$LINENO" "reallocarray" "ac_cv_func_reallocarray"
-if test "x$ac_cv_func_reallocarray" = xyes; then :
- cat >>confdefs.h <<_ACEOF
-#define HAVE_REALLOCARRAY 1
-_ACEOF
-
-fi
-done
-
-
- if test "x$ac_cv_func_reallocarray" = xyes; then
- HAVE_REALLOCARRAY_TRUE=
- HAVE_REALLOCARRAY_FALSE='#'
-else
- HAVE_REALLOCARRAY_TRUE='#'
- HAVE_REALLOCARRAY_FALSE=
-fi
-
- if test "x$ac_cv_func_strchrnul" = xyes; then
- HAVE_STRCHRNUL_TRUE=
- HAVE_STRCHRNUL_FALSE='#'
-else
- HAVE_STRCHRNUL_TRUE='#'
- HAVE_STRCHRNUL_FALSE=
-fi
-
-
-ac_config_headers="$ac_config_headers src/config.h:src/config.hin"
-
-
-ac_config_files="$ac_config_files Makefile docs/andi.1 docs/Makefile libs/Makefile opt/Makefile opt/psufsort/Makefile src/Makefile test/Makefile"
-
-cat >confcache <<\_ACEOF
-# This file is a shell script that caches the results of configure
-# tests run on this system so they can be shared between configure
-# scripts and configure runs, see configure's option --config-cache.
-# It is not useful on other systems. If it contains results you don't
-# want to keep, you may remove or edit it.
-#
-# config.status only pays attention to the cache file if you give it
-# the --recheck option to rerun configure.
-#
-# `ac_cv_env_foo' variables (set or unset) will be overridden when
-# loading this file, other *unset* `ac_cv_foo' will be assigned the
-# following values.
-
-_ACEOF
-
-# The following way of writing the cache mishandles newlines in values,
-# but we know of no workaround that is simple, portable, and efficient.
-# So, we kill variables containing newlines.
-# Ultrix sh set writes to stderr and can't be redirected directly,
-# and sets the high bit in the cache file unless we assign to the vars.
-(
- for ac_var in `(set) 2>&1 | sed -n 's/^\([a-zA-Z_][a-zA-Z0-9_]*\)=.*/\1/p'`; do
- eval ac_val=\$$ac_var
- case $ac_val in #(
- *${as_nl}*)
- case $ac_var in #(
- *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5
-$as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;;
- esac
- case $ac_var in #(
- _ | IFS | as_nl) ;; #(
- BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #(
- *) { eval $ac_var=; unset $ac_var;} ;;
- esac ;;
- esac
- done
-
- (set) 2>&1 |
- case $as_nl`(ac_space=' '; set) 2>&1` in #(
- *${as_nl}ac_space=\ *)
- # `set' does not quote correctly, so add quotes: double-quote
- # substitution turns \\\\ into \\, and sed turns \\ into \.
- sed -n \
- "s/'/'\\\\''/g;
- s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p"
- ;; #(
- *)
- # `set' quotes correctly as required by POSIX, so do not add quotes.
- sed -n "/^[_$as_cr_alnum]*_cv_[_$as_cr_alnum]*=/p"
- ;;
- esac |
- sort
-) |
- sed '
- /^ac_cv_env_/b end
- t clear
- :clear
- s/^\([^=]*\)=\(.*[{}].*\)$/test "${\1+set}" = set || &/
- t end
- s/^\([^=]*\)=\(.*\)$/\1=${\1=\2}/
- :end' >>confcache
-if diff "$cache_file" confcache >/dev/null 2>&1; then :; else
- if test -w "$cache_file"; then
- if test "x$cache_file" != "x/dev/null"; then
- { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5
-$as_echo "$as_me: updating cache $cache_file" >&6;}
- if test ! -f "$cache_file" || test -h "$cache_file"; then
- cat confcache >"$cache_file"
- else
- case $cache_file in #(
- */* | ?:*)
- mv -f confcache "$cache_file"$$ &&
- mv -f "$cache_file"$$ "$cache_file" ;; #(
- *)
- mv -f confcache "$cache_file" ;;
- esac
- fi
- fi
- else
- { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5
-$as_echo "$as_me: not updating unwritable cache $cache_file" >&6;}
- fi
-fi
-rm -f confcache
-
-test "x$prefix" = xNONE && prefix=$ac_default_prefix
-# Let make expand exec_prefix.
-test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
-
-DEFS=-DHAVE_CONFIG_H
-
-ac_libobjs=
-ac_ltlibobjs=
-U=
-for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue
- # 1. Remove the extension, and $U if already installed.
- ac_script='s/\$U\././;s/\.o$//;s/\.obj$//'
- ac_i=`$as_echo "$ac_i" | sed "$ac_script"`
- # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR
- # will be set to the directory where LIBOBJS objects are built.
- as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext"
- as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo'
-done
-LIBOBJS=$ac_libobjs
-
-LTLIBOBJS=$ac_ltlibobjs
-
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking that generated files are newer than configure" >&5
-$as_echo_n "checking that generated files are newer than configure... " >&6; }
- if test -n "$am_sleep_pid"; then
- # Hide warnings about reused PIDs.
- wait $am_sleep_pid 2>/dev/null
- fi
- { $as_echo "$as_me:${as_lineno-$LINENO}: result: done" >&5
-$as_echo "done" >&6; }
- if test -n "$EXEEXT"; then
- am__EXEEXT_TRUE=
- am__EXEEXT_FALSE='#'
-else
- am__EXEEXT_TRUE='#'
- am__EXEEXT_FALSE=
-fi
-
-if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then
- as_fn_error $? "conditional \"AMDEP\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
- as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then
- as_fn_error $? "conditional \"am__fastdepCXX\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${BUILD_WITH_LIBDIVSUFSORT_TRUE}" && test -z "${BUILD_WITH_LIBDIVSUFSORT_FALSE}"; then
- as_fn_error $? "conditional \"BUILD_WITH_LIBDIVSUFSORT\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${BUILD_TESTS_TRUE}" && test -z "${BUILD_TESTS_FALSE}"; then
- as_fn_error $? "conditional \"BUILD_TESTS\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_REALLOCARRAY_TRUE}" && test -z "${HAVE_REALLOCARRAY_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_REALLOCARRAY\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-if test -z "${HAVE_STRCHRNUL_TRUE}" && test -z "${HAVE_STRCHRNUL_FALSE}"; then
- as_fn_error $? "conditional \"HAVE_STRCHRNUL\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
-
-: "${CONFIG_STATUS=./config.status}"
-ac_write_fail=0
-ac_clean_files_save=$ac_clean_files
-ac_clean_files="$ac_clean_files $CONFIG_STATUS"
-{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5
-$as_echo "$as_me: creating $CONFIG_STATUS" >&6;}
-as_write_fail=0
-cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1
-#! $SHELL
-# Generated by $as_me.
-# Run this file to recreate the current configuration.
-# Compiler output produced by configure, useful for debugging
-# configure, is in config.log if it exists.
-
-debug=false
-ac_cs_recheck=false
-ac_cs_silent=false
-
-SHELL=\${CONFIG_SHELL-$SHELL}
-export SHELL
-_ASEOF
-cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1
-## -------------------- ##
-## M4sh Initialization. ##
-## -------------------- ##
-
-# Be more Bourne compatible
-DUALCASE=1; export DUALCASE # for MKS sh
-if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then :
- emulate sh
- NULLCMD=:
- # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which
- # is contrary to our usage. Disable this feature.
- alias -g '${1+"$@"}'='"$@"'
- setopt NO_GLOB_SUBST
-else
- case `(set -o) 2>/dev/null` in #(
- *posix*) :
- set -o posix ;; #(
- *) :
- ;;
-esac
-fi
-
-
-as_nl='
-'
-export as_nl
-# Printing a long string crashes Solaris 7 /usr/bin/printf.
-as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\'
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo
-as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo
-# Prefer a ksh shell builtin over an external printf program on Solaris,
-# but without wasting forks for bash or zsh.
-if test -z "$BASH_VERSION$ZSH_VERSION" \
- && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then
- as_echo='print -r --'
- as_echo_n='print -rn --'
-elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then
- as_echo='printf %s\n'
- as_echo_n='printf %s'
-else
- if test "X`(/usr/ucb/echo -n -n $as_echo) 2>/dev/null`" = "X-n $as_echo"; then
- as_echo_body='eval /usr/ucb/echo -n "$1$as_nl"'
- as_echo_n='/usr/ucb/echo -n'
- else
- as_echo_body='eval expr "X$1" : "X\\(.*\\)"'
- as_echo_n_body='eval
- arg=$1;
- case $arg in #(
- *"$as_nl"*)
- expr "X$arg" : "X\\(.*\\)$as_nl";
- arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;;
- esac;
- expr "X$arg" : "X\\(.*\\)" | tr -d "$as_nl"
- '
- export as_echo_n_body
- as_echo_n='sh -c $as_echo_n_body as_echo'
- fi
- export as_echo_body
- as_echo='sh -c $as_echo_body as_echo'
-fi
-
-# The user is always right.
-if test "${PATH_SEPARATOR+set}" != set; then
- PATH_SEPARATOR=:
- (PATH='/bin;/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 && {
- (PATH='/bin:/bin'; FPATH=$PATH; sh -c :) >/dev/null 2>&1 ||
- PATH_SEPARATOR=';'
- }
-fi
-
-
-# IFS
-# We need space, tab and new line, in precisely that order. Quoting is
-# there to prevent editors from complaining about space-tab.
-# (If _AS_PATH_WALK were called with IFS unset, it would disable word
-# splitting by setting IFS to empty value.)
-IFS=" "" $as_nl"
-
-# Find who we are. Look in the path if we contain no directory separator.
-as_myself=
-case $0 in #((
- *[\\/]* ) as_myself=$0 ;;
- *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
-for as_dir in $PATH
-do
- IFS=$as_save_IFS
- test -z "$as_dir" && as_dir=.
- test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break
- done
-IFS=$as_save_IFS
-
- ;;
-esac
-# We did not find ourselves, most probably we were run as `sh COMMAND'
-# in which case we are not to be found in the path.
-if test "x$as_myself" = x; then
- as_myself=$0
-fi
-if test ! -f "$as_myself"; then
- $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2
- exit 1
-fi
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diff --git a/configure.ac b/configure.ac
index c69acfd..fdf319f 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([andi], [0.9.4])
+AC_INIT([andi], [0.9.5-beta])
AM_INIT_AUTOMAKE([-Wall foreign ])
AC_CONFIG_MACRO_DIR([m4])
@@ -83,7 +83,7 @@ AC_HEADER_STDBOOL
# non-null pointer. This breaks the build on systems using uClibc, including
# my laptop.
# As requesting zero bytes is not useful, and implementation-defined behaviour,
-# I should be avoided in the first place. Thus I really don't need these checks.
+# it should be avoided in the first place. Thus I really don't need these checks.
AC_CHECK_FUNCS([floor pow sqrt strdup strerror])
AC_CHECK_FUNCS([strndup])
diff --git a/depcomp b/depcomp
deleted file mode 100755
index 4ebd5b3..0000000
--- a/depcomp
+++ /dev/null
@@ -1,791 +0,0 @@
-#! /bin/sh
-# depcomp - compile a program generating dependencies as side-effects
-
-scriptversion=2013-05-30.07; # UTC
-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
-
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-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program 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 <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# Originally written by Alexandre Oliva <oliva at dcc.unicamp.br>.
-
-case $1 in
- '')
- echo "$0: No command. Try '$0 --help' for more information." 1>&2
- exit 1;
- ;;
- -h | --h*)
- cat <<\EOF
-Usage: depcomp [--help] [--version] PROGRAM [ARGS]
-
-Run PROGRAMS ARGS to compile a file, generating dependencies
-as side-effects.
-
-Environment variables:
- depmode Dependency tracking mode.
- source Source file read by 'PROGRAMS ARGS'.
- object Object file output by 'PROGRAMS ARGS'.
- DEPDIR directory where to store dependencies.
- depfile Dependency file to output.
- tmpdepfile Temporary file to use when outputting dependencies.
- libtool Whether libtool is used (yes/no).
-
-Report bugs to <bug-automake at gnu.org>.
-EOF
- exit $?
- ;;
- -v | --v*)
- echo "depcomp $scriptversion"
- exit $?
- ;;
-esac
-
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-# global variables '$dir'. Note that this directory component will
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-{
- case $1 in
- */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
- *) dir=;;
- esac
-}
-
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-{
- base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
-}
-
-# If no dependency file was actually created by the compiler invocation,
-# we still have to create a dummy depfile, to avoid errors with the
-# Makefile "include basename.Plo" scheme.
-make_dummy_depfile ()
-{
- echo "#dummy" > "$depfile"
-}
-
-# Factor out some common post-processing of the generated depfile.
-# Requires the auxiliary global variable '$tmpdepfile' to be set.
-aix_post_process_depfile ()
-{
- # If the compiler actually managed to produce a dependency file,
- # post-process it.
- if test -f "$tmpdepfile"; then
- # Each line is of the form 'foo.o: dependency.h'.
- # Do two passes, one to just change these to
- # $object: dependency.h
- # and one to simply output
- # dependency.h:
- # which is needed to avoid the deleted-header problem.
- { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
- sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
- } > "$depfile"
- rm -f "$tmpdepfile"
- else
- make_dummy_depfile
- fi
-}
-
-# A tabulation character.
-tab=' '
-# A newline character.
-nl='
-'
-# Character ranges might be problematic outside the C locale.
-# These definitions help.
-upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
-lower=abcdefghijklmnopqrstuvwxyz
-digits=0123456789
-alpha=${upper}${lower}
-
-if test -z "$depmode" || test -z "$source" || test -z "$object"; then
- echo "depcomp: Variables source, object and depmode must be set" 1>&2
- exit 1
-fi
-
-# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
-depfile=${depfile-`echo "$object" |
- sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
-tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
-
-rm -f "$tmpdepfile"
-
-# Avoid interferences from the environment.
-gccflag= dashmflag=
-
-# Some modes work just like other modes, but use different flags. We
-# parameterize here, but still list the modes in the big case below,
-# to make depend.m4 easier to write. Note that we *cannot* use a case
-# here, because this file can only contain one case statement.
-if test "$depmode" = hp; then
- # HP compiler uses -M and no extra arg.
- gccflag=-M
- depmode=gcc
-fi
-
-if test "$depmode" = dashXmstdout; then
- # This is just like dashmstdout with a different argument.
- dashmflag=-xM
- depmode=dashmstdout
-fi
-
-cygpath_u="cygpath -u -f -"
-if test "$depmode" = msvcmsys; then
- # This is just like msvisualcpp but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvisualcpp
-fi
-
-if test "$depmode" = msvc7msys; then
- # This is just like msvc7 but w/o cygpath translation.
- # Just convert the backslash-escaped backslashes to single forward
- # slashes to satisfy depend.m4
- cygpath_u='sed s,\\\\,/,g'
- depmode=msvc7
-fi
-
-if test "$depmode" = xlc; then
- # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
- gccflag=-qmakedep=gcc,-MF
- depmode=gcc
-fi
-
-case "$depmode" in
-gcc3)
-## gcc 3 implements dependency tracking that does exactly what
-## we want. Yay! Note: for some reason libtool 1.4 doesn't like
-## it if -MD -MP comes after the -MF stuff. Hmm.
-## Unfortunately, FreeBSD c89 acceptance of flags depends upon
-## the command line argument order; so add the flags where they
-## appear in depend2.am. Note that the slowdown incurred here
-## affects only configure: in makefiles, %FASTDEP% shortcuts this.
- for arg
- do
- case $arg in
- -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
- *) set fnord "$@" "$arg" ;;
- esac
- shift # fnord
- shift # $arg
- done
- "$@"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- mv "$tmpdepfile" "$depfile"
- ;;
-
-gcc)
-## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
-## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
-## (see the conditional assignment to $gccflag above).
-## There are various ways to get dependency output from gcc. Here's
-## why we pick this rather obscure method:
-## - Don't want to use -MD because we'd like the dependencies to end
-## up in a subdir. Having to rename by hand is ugly.
-## (We might end up doing this anyway to support other compilers.)
-## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
-## -MM, not -M (despite what the docs say). Also, it might not be
-## supported by the other compilers which use the 'gcc' depmode.
-## - Using -M directly means running the compiler twice (even worse
-## than renaming).
- if test -z "$gccflag"; then
- gccflag=-MD,
- fi
- "$@" -Wp,"$gccflag$tmpdepfile"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- # The second -e expression handles DOS-style file names with drive
- # letters.
- sed -e 's/^[^:]*: / /' \
- -e 's/^['$alpha']:\/[^:]*: / /' < "$tmpdepfile" >> "$depfile"
-## This next piece of magic avoids the "deleted header file" problem.
-## The problem is that when a header file which appears in a .P file
-## is deleted, the dependency causes make to die (because there is
-## typically no way to rebuild the header). We avoid this by adding
-## dummy dependencies for each header file. Too bad gcc doesn't do
-## this for us directly.
-## Some versions of gcc put a space before the ':'. On the theory
-## that the space means something, we add a space to the output as
-## well. hp depmode also adds that space, but also prefixes the VPATH
-## to the object. Take care to not repeat it in the output.
-## Some versions of the HPUX 10.20 sed can't process this invocation
-## correctly. Breaking it into two sed invocations is a workaround.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^\\$//' -e '/^$/d' -e "s|.*$object$||" -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-sgi)
- if test "$libtool" = yes; then
- "$@" "-Wp,-MDupdate,$tmpdepfile"
- else
- "$@" -MDupdate "$tmpdepfile"
- fi
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
-
- if test -f "$tmpdepfile"; then # yes, the sourcefile depend on other files
- echo "$object : \\" > "$depfile"
- # Clip off the initial element (the dependent). Don't try to be
- # clever and replace this with sed code, as IRIX sed won't handle
- # lines with more than a fixed number of characters (4096 in
- # IRIX 6.2 sed, 8192 in IRIX 6.5). We also remove comment lines;
- # the IRIX cc adds comments like '#:fec' to the end of the
- # dependency line.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' \
- | tr "$nl" ' ' >> "$depfile"
- echo >> "$depfile"
- # The second pass generates a dummy entry for each header file.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \
- >> "$depfile"
- else
- make_dummy_depfile
- fi
- rm -f "$tmpdepfile"
- ;;
-
-xlc)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-aix)
- # The C for AIX Compiler uses -M and outputs the dependencies
- # in a .u file. In older versions, this file always lives in the
- # current directory. Also, the AIX compiler puts '$object:' at the
- # start of each line; $object doesn't have directory information.
- # Version 6 uses the directory in both cases.
- set_dir_from "$object"
- set_base_from "$object"
- if test "$libtool" = yes; then
- tmpdepfile1=$dir$base.u
- tmpdepfile2=$base.u
- tmpdepfile3=$dir.libs/$base.u
- "$@" -Wc,-M
- else
- tmpdepfile1=$dir$base.u
- tmpdepfile2=$dir$base.u
- tmpdepfile3=$dir$base.u
- "$@" -M
- fi
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- do
- test -f "$tmpdepfile" && break
- done
- aix_post_process_depfile
- ;;
-
-tcc)
- # tcc (Tiny C Compiler) understand '-MD -MF file' since version 0.9.26
- # FIXME: That version still under development at the moment of writing.
- # Make that this statement remains true also for stable, released
- # versions.
- # It will wrap lines (doesn't matter whether long or short) with a
- # trailing '\', as in:
- #
- # foo.o : \
- # foo.c \
- # foo.h \
- #
- # It will put a trailing '\' even on the last line, and will use leading
- # spaces rather than leading tabs (at least since its commit 0394caf7
- # "Emit spaces for -MD").
- "$@" -MD -MF "$tmpdepfile"
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- # Each non-empty line is of the form 'foo.o : \' or ' dep.h \'.
- # We have to change lines of the first kind to '$object: \'.
- sed -e "s|.*:|$object :|" < "$tmpdepfile" > "$depfile"
- # And for each line of the second kind, we have to emit a 'dep.h:'
- # dummy dependency, to avoid the deleted-header problem.
- sed -n -e 's|^ *\(.*\) *\\$|\1:|p' < "$tmpdepfile" >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-## The order of this option in the case statement is important, since the
-## shell code in configure will try each of these formats in the order
-## listed in this file. A plain '-MD' option would be understood by many
-## compilers, so we must ensure this comes after the gcc and icc options.
-pgcc)
- # Portland's C compiler understands '-MD'.
- # Will always output deps to 'file.d' where file is the root name of the
- # source file under compilation, even if file resides in a subdirectory.
- # The object file name does not affect the name of the '.d' file.
- # pgcc 10.2 will output
- # foo.o: sub/foo.c sub/foo.h
- # and will wrap long lines using '\' :
- # foo.o: sub/foo.c ... \
- # sub/foo.h ... \
- # ...
- set_dir_from "$object"
- # Use the source, not the object, to determine the base name, since
- # that's sadly what pgcc will do too.
- set_base_from "$source"
- tmpdepfile=$base.d
-
- # For projects that build the same source file twice into different object
- # files, the pgcc approach of using the *source* file root name can cause
- # problems in parallel builds. Use a locking strategy to avoid stomping on
- # the same $tmpdepfile.
- lockdir=$base.d-lock
- trap "
- echo '$0: caught signal, cleaning up...' >&2
- rmdir '$lockdir'
- exit 1
- " 1 2 13 15
- numtries=100
- i=$numtries
- while test $i -gt 0; do
- # mkdir is a portable test-and-set.
- if mkdir "$lockdir" 2>/dev/null; then
- # This process acquired the lock.
- "$@" -MD
- stat=$?
- # Release the lock.
- rmdir "$lockdir"
- break
- else
- # If the lock is being held by a different process, wait
- # until the winning process is done or we timeout.
- while test -d "$lockdir" && test $i -gt 0; do
- sleep 1
- i=`expr $i - 1`
- done
- fi
- i=`expr $i - 1`
- done
- trap - 1 2 13 15
- if test $i -le 0; then
- echo "$0: failed to acquire lock after $numtries attempts" >&2
- echo "$0: check lockdir '$lockdir'" >&2
- exit 1
- fi
-
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- # Each line is of the form `foo.o: dependent.h',
- # or `foo.o: dep1.h dep2.h \', or ` dep3.h dep4.h \'.
- # Do two passes, one to just change these to
- # `$object: dependent.h' and one to simply `dependent.h:'.
- sed "s,^[^:]*:,$object :," < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed 's,^[^:]*: \(.*\)$,\1,;s/^\\$//;/^$/d;/:$/d' < "$tmpdepfile" \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-hp2)
- # The "hp" stanza above does not work with aCC (C++) and HP's ia64
- # compilers, which have integrated preprocessors. The correct option
- # to use with these is +Maked; it writes dependencies to a file named
- # 'foo.d', which lands next to the object file, wherever that
- # happens to be.
- # Much of this is similar to the tru64 case; see comments there.
- set_dir_from "$object"
- set_base_from "$object"
- if test "$libtool" = yes; then
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir.libs/$base.d
- "$@" -Wc,+Maked
- else
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir$base.d
- "$@" +Maked
- fi
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile1" "$tmpdepfile2"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2"
- do
- test -f "$tmpdepfile" && break
- done
- if test -f "$tmpdepfile"; then
- sed -e "s,^.*\.[$lower]*:,$object:," "$tmpdepfile" > "$depfile"
- # Add 'dependent.h:' lines.
- sed -ne '2,${
- s/^ *//
- s/ \\*$//
- s/$/:/
- p
- }' "$tmpdepfile" >> "$depfile"
- else
- make_dummy_depfile
- fi
- rm -f "$tmpdepfile" "$tmpdepfile2"
- ;;
-
-tru64)
- # The Tru64 compiler uses -MD to generate dependencies as a side
- # effect. 'cc -MD -o foo.o ...' puts the dependencies into 'foo.o.d'.
- # At least on Alpha/Redhat 6.1, Compaq CCC V6.2-504 seems to put
- # dependencies in 'foo.d' instead, so we check for that too.
- # Subdirectories are respected.
- set_dir_from "$object"
- set_base_from "$object"
-
- if test "$libtool" = yes; then
- # Libtool generates 2 separate objects for the 2 libraries. These
- # two compilations output dependencies in $dir.libs/$base.o.d and
- # in $dir$base.o.d. We have to check for both files, because
- # one of the two compilations can be disabled. We should prefer
- # $dir$base.o.d over $dir.libs/$base.o.d because the latter is
- # automatically cleaned when .libs/ is deleted, while ignoring
- # the former would cause a distcleancheck panic.
- tmpdepfile1=$dir$base.o.d # libtool 1.5
- tmpdepfile2=$dir.libs/$base.o.d # Likewise.
- tmpdepfile3=$dir.libs/$base.d # Compaq CCC V6.2-504
- "$@" -Wc,-MD
- else
- tmpdepfile1=$dir$base.d
- tmpdepfile2=$dir$base.d
- tmpdepfile3=$dir$base.d
- "$@" -MD
- fi
-
- stat=$?
- if test $stat -ne 0; then
- rm -f "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- exit $stat
- fi
-
- for tmpdepfile in "$tmpdepfile1" "$tmpdepfile2" "$tmpdepfile3"
- do
- test -f "$tmpdepfile" && break
- done
- # Same post-processing that is required for AIX mode.
- aix_post_process_depfile
- ;;
-
-msvc7)
- if test "$libtool" = yes; then
- showIncludes=-Wc,-showIncludes
- else
- showIncludes=-showIncludes
- fi
- "$@" $showIncludes > "$tmpdepfile"
- stat=$?
- grep -v '^Note: including file: ' "$tmpdepfile"
- if test $stat -ne 0; then
- rm -f "$tmpdepfile"
- exit $stat
- fi
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- # The first sed program below extracts the file names and escapes
- # backslashes for cygpath. The second sed program outputs the file
- # name when reading, but also accumulates all include files in the
- # hold buffer in order to output them again at the end. This only
- # works with sed implementations that can handle large buffers.
- sed < "$tmpdepfile" -n '
-/^Note: including file: *\(.*\)/ {
- s//\1/
- s/\\/\\\\/g
- p
-}' | $cygpath_u | sort -u | sed -n '
-s/ /\\ /g
-s/\(.*\)/'"$tab"'\1 \\/p
-s/.\(.*\) \\/\1:/
-H
-$ {
- s/.*/'"$tab"'/
- G
- p
-}' >> "$depfile"
- echo >> "$depfile" # make sure the fragment doesn't end with a backslash
- rm -f "$tmpdepfile"
- ;;
-
-msvc7msys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-#nosideeffect)
- # This comment above is used by automake to tell side-effect
- # dependency tracking mechanisms from slower ones.
-
-dashmstdout)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout, regardless of -o.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove '-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- test -z "$dashmflag" && dashmflag=-M
- # Require at least two characters before searching for ':'
- # in the target name. This is to cope with DOS-style filenames:
- # a dependency such as 'c:/foo/bar' could be seen as target 'c' otherwise.
- "$@" $dashmflag |
- sed "s|^[$tab ]*[^:$tab ][^:][^:]*:[$tab ]*|$object: |" > "$tmpdepfile"
- rm -f "$depfile"
- cat < "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process this sed invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- tr ' ' "$nl" < "$tmpdepfile" \
- | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-dashXmstdout)
- # This case only exists to satisfy depend.m4. It is never actually
- # run, as this mode is specially recognized in the preamble.
- exit 1
- ;;
-
-makedepend)
- "$@" || exit $?
- # Remove any Libtool call
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
- # X makedepend
- shift
- cleared=no eat=no
- for arg
- do
- case $cleared in
- no)
- set ""; shift
- cleared=yes ;;
- esac
- if test $eat = yes; then
- eat=no
- continue
- fi
- case "$arg" in
- -D*|-I*)
- set fnord "$@" "$arg"; shift ;;
- # Strip any option that makedepend may not understand. Remove
- # the object too, otherwise makedepend will parse it as a source file.
- -arch)
- eat=yes ;;
- -*|$object)
- ;;
- *)
- set fnord "$@" "$arg"; shift ;;
- esac
- done
- obj_suffix=`echo "$object" | sed 's/^.*\././'`
- touch "$tmpdepfile"
- ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@"
- rm -f "$depfile"
- # makedepend may prepend the VPATH from the source file name to the object.
- # No need to regex-escape $object, excess matching of '.' is harmless.
- sed "s|^.*\($object *:\)|\1|" "$tmpdepfile" > "$depfile"
- # Some versions of the HPUX 10.20 sed can't process the last invocation
- # correctly. Breaking it into two sed invocations is a workaround.
- sed '1,2d' "$tmpdepfile" \
- | tr ' ' "$nl" \
- | sed -e 's/^\\$//' -e '/^$/d' -e '/:$/d' \
- | sed -e 's/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile" "$tmpdepfile".bak
- ;;
-
-cpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- # Remove '-o $object'.
- IFS=" "
- for arg
- do
- case $arg in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift # fnord
- shift # $arg
- ;;
- esac
- done
-
- "$@" -E \
- | sed -n -e '/^# [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- -e '/^#line [0-9][0-9]* "\([^"]*\)".*/ s:: \1 \\:p' \
- | sed '$ s: \\$::' > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- cat < "$tmpdepfile" >> "$depfile"
- sed < "$tmpdepfile" '/^$/d;s/^ //;s/ \\$//;s/$/ :/' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvisualcpp)
- # Important note: in order to support this mode, a compiler *must*
- # always write the preprocessed file to stdout.
- "$@" || exit $?
-
- # Remove the call to Libtool.
- if test "$libtool" = yes; then
- while test "X$1" != 'X--mode=compile'; do
- shift
- done
- shift
- fi
-
- IFS=" "
- for arg
- do
- case "$arg" in
- -o)
- shift
- ;;
- $object)
- shift
- ;;
- "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI")
- set fnord "$@"
- shift
- shift
- ;;
- *)
- set fnord "$@" "$arg"
- shift
- shift
- ;;
- esac
- done
- "$@" -E 2>/dev/null |
- sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile"
- rm -f "$depfile"
- echo "$object : \\" > "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::'"$tab"'\1 \\:p' >> "$depfile"
- echo "$tab" >> "$depfile"
- sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile"
- rm -f "$tmpdepfile"
- ;;
-
-msvcmsys)
- # This case exists only to let depend.m4 do its work. It works by
- # looking at the text of this script. This case will never be run,
- # since it is checked for above.
- exit 1
- ;;
-
-none)
- exec "$@"
- ;;
-
-*)
- echo "Unknown depmode $depmode" 1>&2
- exit 1
- ;;
-esac
-
-exit 0
-
-# Local Variables:
-# mode: shell-script
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diff --git a/docs/andi.1 b/docs/andi.1
deleted file mode 100644
index 4b4facc..0000000
--- a/docs/andi.1
+++ /dev/null
@@ -1,56 +0,0 @@
-.TH ANDI "1" "June 2015" "0.9.4" ""
-.SH NAME
-andi \- estimates evolutionary distance
-.SH SYNOPSIS
-.B andi
-[\fI-jrv\fR] [\fI-p FLOAT\fR] [\fI-t INT\fR] \fIFILES\fR...
-.SH DESCRIPTION
-.TP
-\fBandi\fR estimates the evolutionary distance between closely related genomes. For this \fBandi\fR reads the input sequences from \fIFASTA\fR files and computes the pairwise anchor distance. The idea behind this is explained in a paper by Haubold et al. (see below).
-.SH OUTPUT
-The output is a symmetrical distance matrix in \fIPHYLIP\fR format, with each entry representing divergence with a positive real number. A distance of zero means that two sequences are identical, whereas other values are estimates for the nucleotide substitution rate (Jukes-Cantor corrected). For technical reasons the comparison might fail and no estimate can be computed. In such cases \fInan\fR is printed. This either means that the input sequences were too short (<200bp) or too diverse [...]
-.SH OPTIONS
-.TP
-\fB\-j\fR, \fB\-\-join\fR
-Use this mode if each of your \fIFASTA\fR files represents one assembly with numerous contigs. \fBandi\fR will then treat all of the contained sequences per file as a single genome. In this mode at least one file name must be provided via command line arguments. For the output the filename is used to identify each sequence.
-.TP
-\fB\-m\fR, \fB\-\-low-memory\fR
-In multithreaded mode, \fBandi\fR requires memory linear to the amount of threads. The low memory mode changes this to a constant demand independent from the used number of threads. Unfortunately, this comes at a significant runtime cost.
-.TP
-\fB\-p\fR <FLOAT>
-Significance of an anchor pair; default: 0.05.
-.TP
-\fB\-r\fR, \fB\-\-raw\fR
-Calculates raw distances; default: Jukes\-Cantor corrected.
-.TP
-\fB\-t\fR <INT>
-The number of threads to be used; by default, all available processors are used.
-.br
-Multithreading is only available if \fBandi\fR was compiled with OpenMP support.
-.TP
-\fB\-v\fR, \fB\-\-verbose\fR
-Prints additional information. Apply multiple times for extra verboseness.
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-Prints the synopsis and an explanation of available options.
-.TP
-\fB\-\-version\fR
-Outputs version information and acknowledgments.
-.SH COPYRIGHT
-Copyright \(co 2014, 2015 Fabian Klötzl
-License GPLv3+: GNU GPL version 3 or later.
-.br
-This is free software: you are free to change and redistribute it.
-There is NO WARRANTY, to the extent permitted by law.
-The full license text is available at <http://gnu.org/licenses/gpl.html>.
-.PP
-.SH ACKNOWLEDGMENTS
-1) andi: Haubold, B. Klötzl, F. and Pfaffelhuber, P. (2015). andi: Fast and accurate estimation of evolutionary distances between closely related genomes
-.br
-2) Algorithms: Ohlebusch, E. (2013). Bioinformatics Algorithms. Sequence Analysis, Genome Rearrangements, and Phylogenetic Reconstruction. pp 118f.
-.br
-3) SA construction: Mori, Y. (2005). Short description of improved two\-stage suffix sorting algorithm. http://homepage3.nifty.com/wpage/software/itssort.txt
-.SH BUGS
-.SS Reporting Bugs
-Please report bugs to <kloetzl at evolbio.mpg.de> or at <https://github.com/EvolBioInf/andi>.
-.SS
diff --git a/docs/manual/andi-manual.tex b/docs/manual/andi-manual.tex
new file mode 100644
index 0000000..2a60356
--- /dev/null
+++ b/docs/manual/andi-manual.tex
@@ -0,0 +1,386 @@
+\documentclass[a4paper,
+ 10pt,
+ english,
+ DIV=12,
+ BCOR=8mm]{scrbook}
+\usepackage[utf8x]{inputenc}
+\usepackage{babel}
+\usepackage{listings}
+\usepackage{xcolor}
+\usepackage{hyperref}
+\usepackage{siunitx}
+\usepackage[T1]{fontenc}
+\usepackage{isodate}
+\usepackage{graphicx}
+\usepackage{amsthm}
+\usepackage{acronym}
+\usepackage{amssymb}
+\usepackage{tikz}
+\usepackage{pgfplots}
+\usepackage{caption}
+\usepackage{subcaption}
+\usepackage{booktabs}
+\usepackage{xspace}
+\usepackage{overpic}
+
+\bibliographystyle{alpha}
+
+\DeclareSIUnit\byte{B}
+\DeclareSIUnit\basepairs{bp}
+\DeclareSIUnit\bit{bit}
+
+\definecolor{oceangreen}{cmyk}{1,.0,.20,.78}
+\addtokomafont{sectioning}{\rmfamily\color{oceangreen}}
+
+\definecolor{bluekeywords}{rgb}{0.13,0.13,1}
+\definecolor{greencomments}{rgb}{0,0.5,0}
+\definecolor{turqusnumbers}{rgb}{0.17,0.57,0.69}
+\definecolor{redstrings}{rgb}{0.5,0,0}
+\definecolor{lightgray}{rgb}{0.9,0.9,0.9}
+
+\usepackage{libertine}
+\fontfamily{libertine}
+\selectfont
+%\usepackage[scaled]{berasans}
+
+\newcommand{\thymine}{\textsc{m}\oldstylenums{2}\xspace}
+\newcommand{\local}{\textsc{m}\oldstylenums{1}\xspace}
+\newcommand{\algo}[1]{\textsc{{#1}}}
+\newcommand{\andi}{\algo{andi} }
+\newcommand{\word}[1]{\textsf{\small#1}}
+\newcommand{\wchar}[1]{\textsf{\small#1}}
+\newcommand{\eco}{\textsc{eco}\oldstylenums{29}\xspace}
+\newcommand{\pneu}{\textsc{Pneu}\oldstylenums{3085}\xspace}
+
+\include{version}
+
+% Todos at the margin
+\newcommand{\todo}[1]{
+ \marginpar{\fbox{\begin{minipage}{0.9\marginparwidth}
+ \scriptsize\sloppy\raggedright #1
+ \end{minipage}}}
+}
+
+
+\newtheorem{definition}{Definition}
+
+
+\lstset{backgroundcolor=\color{lightgray}}
+
+\lstdefinestyle{shell}{
+ language=bash,
+ columns=flexible,
+ xleftmargin=12pt,
+ xrightmargin=12pt,
+ breaklines=true,
+ basicstyle=\small\ttfamily,
+ morekeywords={make, tar, git, sudo, andi, time, man, head, cut, fneighbor, fretree, figtree},
+ % literate={~} {$\sim$}{1}
+}
+
+\lstset{style=shell}
+
+\title{Documentation of \algo{andi}}
+\subtitle{Rapid Estimation of Evolutionary Distances between Genomes\\ {\small\url{https://github.com/EvolBioInf/andi}}}
+\author{Fabian Klötzl\\ \href{mailto:kloetzl at evolbio.mpg.de}{kloetzl at evolbio.mpg.de}}
+\date{Version \version, \isodate\today \\
+\vspace*{2cm}
+\centering\includegraphics[width=0.8\textwidth]{andi_labels.pdf}}
+
+\begin{document}
+
+\maketitle
+
+\section*{Abstract}
+This is the documentation of the \andi program for estimating the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because \andi does not compute full alignments, it is so efficient that it scales well up to thousands of bacterial genomes.
+
+This is scientific software. Please cite our paper \cite{andi} if you use \andi in your publication. Also refer to the paper for the iterna of \andi. Additionally, there is a Master's thesis with even more in depth analysis of \andi \cite{kloetzl}.
+
+\vspace*{1cm}
+\section*{License}
+This document is release under the Creative Commons Attribution Share-Alike license. This means, you are free to copy and redistribute this document. You may even remix, tweak and build upon this document, as long as you credit me for the work I've done and release your document under the identical terms. The full legal code is available online: {\small\url{https://creativecommons.org/licenses/by-sa/4.0/legalcode}}.
+
+\tableofcontents
+
+\chapter{Installation} %%%%%
+
+The easiest way to obtain your own copy of \algo{andi}, is to download the latest \href{https://github.com/EvolBioInf/andi/releases}{release} from GitHub. Please note, that \andi requires \algo{libdivsufsort}\footnote{\url{https://github.com/y-256/libdivsufsort}} for optimal performance \cite{divsufsort}. If you wish to install \andi without \algo{libdivsufsort}, consult Section~\ref{sub:wo-divsufsort}.
+
+\andi runs best under a \algo{Unix} commandline such as \lstinline$bash$. All following examples are also intended for that environment.
+
+\section{Installing from Source Package} \label{sub:regular}
+
+Once you have downloaded the package, unzip it and change into the newly created directory.
+
+\begin{lstlisting}
+~ % tar -xzvf andi-0.9.tar.gz
+~ % cd andi-0.9
+\end{lstlisting}
+
+\noindent Now build and install \andi.
+
+\begin{lstlisting}
+~/andi-0.9 % ./configure
+~/andi-0.9 % make
+~/andi-0.9 % sudo make install
+\end{lstlisting}
+
+\noindent This installs \andi for all users on your system. If you do not have root privileges, you will find a working copy of \andi in the \lstinline$src$ subdirectory. For the rest of this documentation, I will assume, that \andi is in your \textdollar\lstinline!PATH!.
+
+Now \andi should be ready for use. Try invoking the help.
+
+\begin{lstlisting}
+~/andi-0.9 % andi -h
+Usage: andi [-jrv] [-p FLOAT] FILES...
+ FILES... can be any sequence of FASTA files. If no files are supplied, stdin is used instead.
+Options:
+ -j, --join Treat all sequences from one file as a single genome
+ -m, --low-memory Use less memory at the cost of speed
+ -p <FLOAT> Significance of an anchor pair; default: 0.05
+ -r, --raw Calculates raw distances; default: Jukes-Cantor corrected
+ -v, --verbose Prints additional information
+ -t <INT> The number of threads to be used; default: 1
+ -h, --help Display this help and exit
+ --version Output version information and acknowledgments
+\end{lstlisting}
+
+\noindent \andi also comes with a man page, which can be accessed via \lstinline$man andi$. % But once you are done with this documentation, you will require it scarcely.
+
+\section{Installing without \algo{libdivsufsort}} \label{sub:wo-divsufsort}
+
+In case you cannot or do not want to install \algo{libdivsufsort}, \andi comes with its own implementation of a \emph{suffix array construction algorithm}. It is called \algo{psufsort} and is also available, separately.\footnote{\url{https://github.com/kloetzl/psufsort}} To activate it for \algo{andi}, proceed as described in Section~\ref{sub:regular}, but with the following twist:
+
+\begin{lstlisting}
+~/andi % ./configure --without-libdivsufsort
+\end{lstlisting}
+
+Please note that this requires a C++11 compiler. Also, \algo{psufsort} may be slower than \algo{libdivsufsort} and thus lead to inferior runtimes.
+
+\section{Installing from Git Repository}
+
+To build \andi from the \algo{Git} repo, you will also need the \algo{autotools}. Refer to your OS documentation for installation instructions. Once done, execute the following steps.
+
+\begin{lstlisting}
+~ % git clone git at github.com:EvolBioInf/andi.git
+~ % cd andi
+~/andi % autoreconf -i
+\end{lstlisting}
+
+\noindent For old versions of \algo{autoconf} you may instead have to use \lstinline$autoreconf -i -Im4$.
+
+\noindent Continue with the \algo{Gnu} trinity as described in Section~\ref{sub:regular}.
+
+
+\chapter{Usage} %%%%%
+
+The input sequences for \andi should be in \algo{Fasta} format. Any number of files can be passed. Each file may contain more than one sequence.
+
+\begin{lstlisting}
+~ % andi S1.fasta S2.fasta
+2
+S1 0.0000 0.0979
+S2 0.0979 0.0000
+\end{lstlisting}
+
+If no file argument is given, \andi reads the input from \algo{stdin}. This makes it convenient to use in \algo{Unix} pipelines.
+
+\begin{lstlisting}
+~ % cat S1.fasta S2.fasta | andi
+2
+S1 0.0000 0.0979
+S2 0.0979 0.0000
+\end{lstlisting}
+
+The output of \andi is a matrix in \algo{Phylip} style: On the first line the number of compared sequences is given, \lstinline!2! in our example. Then the matrix is printed, where each line is preceded by the name of the $i$th sequence. Note that the matrix is symmetric and the main diagonal contains only zeros. The numbers themselves are evolutionary distances, estimates as substitution rates.
+
+
+\section{Input} \label{sec:join}
+
+As mentioned before, \andi reads in \algo{Fasta} files. It recognizes only the four standard bases and is case insensitive (RegEx: \lstinline![acgtACGT]!). All other residue symbols are excluded from the analysis and \andi prints a warning, when this happens.
+
+If instead of distinct sequences, a \algo{Fasta} file contains contigs belonging to a single taxon, \andi will treat them as a unit when switched into \algo{join} mode. This can be achieved by using the \lstinline!-j! or \lstinline!--join! command line switch.
+
+\begin{lstlisting}
+~ % andi --join E_coli.fasta Shigella.fasta
+[Output]
+\end{lstlisting}
+
+When the \algo{join} mode is active, the file names are used to label the individual sequences. Thus, in \algo{join} mode, each genome has to be in its own file, and furthermore, at least one filename has to be given via the command line.
+
+If \andi seems to take unusually long, or requires huge amounts of memory, then you might have forgotten the \algo{join} switch. This makes \andi compare each contig instead of each genome, resulting in many more comparisons! To make \andi output the number of genome it about to compare, use the \lstinline$--verbose$ switch.
+
+\section{Output}
+
+The output of \andi is written to \lstinline$stdout$. This makes it easy to use on the command line and within shell scripts. As seen before, the matrix, computed by \algo{andi}, is given in \algo{Phylip} format \cite{phylip}.
+
+\begin{lstlisting}
+~ % cat S1.fasta S2.fasta | andi
+2
+S1 0.0000 0.0979
+S2 0.0979 0.0000
+\end{lstlisting}
+
+If the computation completed successfully, \andi exits with the status code 0. Otherwise, the value of \lstinline$errno$ is used as the exit code. \andi can also produce warnings and error messages for the user's convenience. These messages are printed to \lstinline$stderr$ and thus do not interfere with the normal output.
+
+\section{Options}
+
+\andi takes a small number of commandline options, of which even fewer are of interest on a day-to-day basis. If \lstinline$andi -h$ displays a \lstinline$-t$ option, then \andi was compiled with multi-threading support (implemented using \algo{OpenMP}). By default \andi uses all available processors. However, to restrict the number of threads, use \lstinline$-t$.
+
+\begin{lstlisting}
+~ % time andi ../test/1M.1.fasta -t 1
+2
+S1 0.0000 0.0995
+S2 0.0995 0.0000
+./andi ../test/1M.1.fasta 0,60s user 0,01s system 99% cpu 0,613 total
+~ % time andi ../test/1M.1.fasta -t 2
+2
+S1 0.0000 0.0995
+S2 0.0995 0.0000
+./andi ../test/1M.1.fasta -t 2 0,67s user 0,03s system 195% cpu 0,362 total
+\end{lstlisting}
+
+In the above examples the runtime dropped from \SI{0.613}{\second}, to \SI{0.362}{\second} using two threads. Giving \andi more threads than input genomes leads to no further speed improvement. \, The other important option is \lstinline$--join$ (see Section~\ref{sec:join}).
+
+By default, the distances computed by \andi are \emph{Jukes-Cantor} corrected \cite{jukescantor}. This means, the output is substitution rates, which is greater than the mismatch rate. To obtain the pure mismatch rate, use the \lstinline$--raw$ switch.
+
+\section{Example: \algo{eco29}}
+
+Here follows a real-world example of how to use \algo{andi}. It makes heavy use of the commandline and tools like \algo{Phylip}. If you prefer \algo{R}, check out this excellent \href{http://holtlab.net/2015/05/08/r-code-to-infer-tree-from-andi-output/}{blog post} by Kathryn Holt.
+
+As a data set we use \algo{eco29}; 29 genomes of \textit{E. Coli} and \textit{Shigella}. You can download the data here: {\small{\url{http://guanine.evolbio.mpg.de/andi/eco29.fasta.gz}}}. The genomes have an average length of 4.9~million nucleotides amounting to a total \SI{138}{\mega\byte}.
+
+\algo{eco29} comes a single \algo{fasta} file, where each sequence is a genome. To calculate their pairwise distances, enter
+
+\begin{lstlisting}
+~ % andi eco29.fasta > eco29.mat
+andi: The input sequences contained characters other than acgtACGT. These were automatically stripped to ensure correct results.
+\end{lstlisting}
+
+\noindent The \algo{eco29} data set includes non-canonical nucleotides, such as \word{Y}, \word{N}, and \word{P}, which get stripped from the input sequences. The resulting matrix is stored in \lstinline$eco29.mat$; Here is a small excerpt:
+
+\begin{lstlisting}
+~ % head -n 5 eco29.mat | cut -d ' ' -f 1-5
+29
+gi|563845 0.0000e+00 1.8388e-02 1.8439e-02 2.6398e-02
+gi|342360 1.8388e-02 0.0000e+00 4.4029e-04 2.6166e-02
+gi|300439 1.8439e-02 4.4029e-04 0.0000e+00 2.6123e-02
+gi|261117 2.6398e-02 2.6166e-02 2.6123e-02 0.0000e+00
+\end{lstlisting}
+
+\noindent From this we compute a tree via neighbor-joining using a \algo{Phylip} wrapper called \algo{Embassy}.\footnote{\url{http://emboss.sourceforge.net/embassy/\#PHYLIP}}
+
+\begin{lstlisting}
+~ % fneighbor -datafile eco29.mat -outfile eco29.phylipdump
+\end{lstlisting}
+\noindent To make this tree easier to read, we can midpoint-root it.
+\begin{lstlisting}
+~ % fretree -spp 29 -intreefile eco29.treefile -outtreefile eco29.tree <<EOF
+M
+X
+Y
+R
+EOF
+\end{lstlisting}
+
+\noindent The file \lstinline$eco29.tree$ now contains the tree in Newick format. This can be plotted using \cite{figtree}
+
+\begin{lstlisting}
+~ % figtree eco29.tree &
+\end{lstlisting}
+
+\noindent to yield
+
+\begin{figure}[h]
+ \centering\includegraphics[width=0.8\textwidth]{andi_labels.pdf}
+\end{figure}
+
+
+
+
+\chapter{DevOps} %%%%%
+
+\andi is written in C/C++; mostly C99 with some parts in C++11. The sources are released on \algo{GitHub} as \emph{free software} under the \textsc{Gnu General Public License version~3} \cite{GPL}. Prebundled packages using \algo{autoconf} are also available, with the latest release being {v0.9} at the time of writing.
+
+If you are interested in the internals of \andi, consult the paper \cite{andi} or my master thesis \cite{kloetzl}. Both explain the used approach in detail. The latter emphasizes the used algorithms, data structures and their efficient implementation.
+
+\section{Dependencies}
+
+Here is a complete list of dependencies required for developing \algo{andi}.
+
+\begin{itemize}
+ \item A C and a C++11 compiler,
+ \item the \algo{autotools},
+ \item \algo{Pdflatex} with various packages for the manual,
+ \item \algo{Git},
+ \item \algo{glib2} for the unit tests,
+ \item \algo{doxygen},
+ \item and \algo{libdivsufsort}.
+\end{itemize}
+
+
+\section{Code Documentation}
+
+\emph{Every} function in \andi is documented using \algo{doxygen} style comments. To create the documentation run \lstinline$make code-docs$ in the main directory. You will then find the documentation under \lstinline$./docs$.
+
+
+\section{Unit Tests}
+
+The unit tests are located in the \andi repository under the \lstinline$./test$ directory. Because they require \algo{glib2}, and a C++11 compiler, they are deactivated by default. To enable them, execute
+
+\begin{lstlisting}
+~/andi % ./configure --enable-unit-tests
+\end{lstlisting}
+
+\noindent during the installation process. You can then verify the build via
+
+\begin{lstlisting}
+~/andi % make check
+\end{lstlisting}
+
+\noindent The unit tests are also checked each time a commit is sent to the repository. This is done via \algo{TravisCI}.\footnote{\url{https://travis-ci.org/EvolBioInf/andi}} Thus, a warning is produced, when the builds fail, or the unit tests to not run successfully. Currently, the unit tests cover more than 80\% of the code. This is computed via the \algo{Travis} builds and a service called \algo{Coveralls}.\footnote{\url{https://coveralls.io/r/EvolBioInf/andi}}
+
+\section{Known Issues}
+
+These minor issues are known. I intend to fix them, when I have time.
+
+\begin{enumerate}
+ \item This code will not work under Windows. At two places Unix-only code is used: filepath-seperators are assumed to be / and file-descriptors are used for I/O.
+\end{enumerate}
+
+
+\section{Creating a Release}
+
+A release should be a stable version of \andi with significant improvements over the last version. For bug fixes, dotdot release may be used.
+
+%\subsection{Preparing a new Release}
+
+Once \andi is matured, the new features implemented, and all tests were run, a new release can be created. First, increase the version number in \lstinline$configure.ac$. Commit that change in git, and tag this commit with \lstinline$vX.y$. Create another commit, where you set the version number to the next release (e.\,g., \lstinline$vX.z-beta$). This assures that there is only one commit and build with that specific version. Now return to the previous commit \lstinline$git checkout vX.y$.
+
+Ensure that \andi is ready for packaging with \algo{autoconf}.
+
+\begin{lstlisting}
+~ % make distcheck
+make dist-gzip am__post_remove_distdir='@:'
+make[1]: Entering directory `/home/kloetzl/Projects/andi'
+if test -d "andi-0.9.1-beta"; then find "andi-0.9.1-beta" -type d ! -perm -200 -exec chmod u+w {} ';' && rm -rf "andi-0.9.1-beta" || { sleep 5 && rm -rf "andi-0.9.1-beta"; }; else :; fi
+test -d "andi-0.9.1-beta" || mkdir "andi-0.9.1-beta"
+ (cd src && make top_distdir=../andi-0.9.1-beta distdir=../andi-0.9.1-beta/src \
+ am__remove_distdir=: am__skip_length_check=: am__skip_mode_fix=: distdir)
+
+... Loads of output ...
+
+=================================================
+andi-0.9.1-beta archives ready for distribution:
+andi-0.9.1-beta.tar.gz
+=================================================
+\end{lstlisting}
+
+If the command does not build successfully, no tarballs will be created. This may necessitate further study of \algo{autoconf} and \algo{automake}.
+
+
+
+\backmatter
+%\addcontentsline{toc}{chapter}{Bibliography}
+\bibliography{references}
+
+\end{document}
diff --git a/docs/manual/andi_labels.pdf b/docs/manual/andi_labels.pdf
new file mode 100644
index 0000000..0c0cc13
Binary files /dev/null and b/docs/manual/andi_labels.pdf differ
diff --git a/docs/manual/references.bib b/docs/manual/references.bib
new file mode 100644
index 0000000..cc2cff6
--- /dev/null
+++ b/docs/manual/references.bib
@@ -0,0 +1,112 @@
+ at misc{divsufsort,
+ author="Yuta Mori",
+ year="2005",
+ title="Short description of improved two-stage suffix sorting algorithm",
+ note="\url{http://homepage3.nifty.com/wpage/software/itssort.txt}"
+}
+
+ at article{andi,
+ author = {Haubold, Bernhard and Klötzl, Fabian and Pfaffelhuber, Peter},
+ title = {andi: Fast and accurate estimation of evolutionary distances between closely related genomes},
+ volume = {31},
+ number = {8},
+ pages = {1169-1175},
+ year = {2015},
+ doi = {10.1093/bioinformatics/btu815},
+ URL = {http://bioinformatics.oxfordjournals.org/content/31/8/1169.abstract},
+ eprint = {http://bioinformatics.oxfordjournals.org/content/31/8/1169.full.pdf+html},
+ journal = {Bioinformatics}
+}
+
+ at book{Felsenstein,
+ author={Joseph Felsenstein},
+ title={Inferring Phylogenies},
+ year={2004},
+ publisher={Sinauer Associates, Inc.}
+}
+
+ at misc{GPL,
+ author={{Free~Software~Foundation}},
+ year={2007},
+ title={Gnu General Public License},
+ note={\url{https://gnu.org/licenses/gpl.html}}
+}
+
+ at misc{phylip,
+ author={Felsenstein, J.},
+ year={2005},
+ title={PHYLIP (Phylogeny Inference Package)},
+ version={version 3.6},
+ howpublished={Distributed by the author},
+ note={Department of Genome Sciences, University of Washington.}
+}
+
+ at InProceedings{LLVM,
+ Author = {Chris Lattner and Vikram Adve},
+ Title = {{LLVM}: A Compilation Framework for Lifelong Program
+ Analysis and Transformation},
+ Booktitle = "Code Generation and Optimizatio",
+ Month = {Mar},
+ Year = {2004},
+ pages = {75--88},
+ Publisher={International Symposium on Code Generation and Optimization}
+}
+
+ at article{ms,
+ author = {Hudson, Richard R.},
+ title = {Generating samples under a Wright–Fisher neutral model of genetic variation},
+ volume = {18},
+ number = {2},
+ pages = {337-338},
+ year = {2002},
+ doi = {10.1093/bioinformatics/18.2.337},
+ URL = {http://bioinformatics.oxfordjournals.org/content/18/2/337.abstract},
+ eprint = {http://bioinformatics.oxfordjournals.org/content/18/2/337.full.pdf+html},
+ journal = {Bioinformatics}
+}
+
+ at article{valgrind,
+ author = {Nethercote, Nicholas and Seward, Julian},
+ title = {Valgrind: A Framework for Heavyweight Dynamic Binary Instrumentation},
+ journal = {SIGPLAN Not.},
+ issue_date = {June 2007},
+ volume = {42},
+ number = {6},
+ month = jun,
+ year = {2007},
+ issn = {0362-1340},
+ pages = {89--100},
+ numpages = {12},
+ url = {http://doi.acm.org/10.1145/1273442.1250746},
+ doi = {10.1145/1273442.1250746},
+ acmid = {1250746},
+ publisher = {ACM},
+ keywords = {Memcheck, Valgrind, dynamic binary analysis, dynamic binary instrumentation, shadow values}
+}
+
+ at misc{figtree,
+ title="FigTree",
+ author={Andrew Rambaut},
+ year={accessed 2015},
+ note={\url{http://tree.bio.ed.ac.uk/software/figtree/}}
+}
+
+
+ at article{jukescantor,
+ author={Jukes, T. H. and Cantor, C. R.},
+ year={1969},
+ title={Evolution of protein molecules},
+ journal={Mammalian protein metabolism},
+ volume={3},
+ pages={21-132},
+ publisher={Academic Press}
+}
+
+ at mastersthesis{kloetzl,
+ author={Fabian Kl{\"o}tzl},
+ school={University of L\"ubeck},
+ year={2015},
+ title={Efficient Estimation of Evolutionary Distances}
+}
+
+
diff --git a/docs/manual/version.tex.in b/docs/manual/version.tex.in
new file mode 100644
index 0000000..565bf96
--- /dev/null
+++ b/docs/manual/version.tex.in
@@ -0,0 +1,2 @@
+
+\newcommand{\version}{VERSION}
diff --git a/install-sh b/install-sh
deleted file mode 100755
index 377bb86..0000000
--- a/install-sh
+++ /dev/null
@@ -1,527 +0,0 @@
-#!/bin/sh
-# install - install a program, script, or datafile
-
-scriptversion=2011-11-20.07; # UTC
-
-# This originates from X11R5 (mit/util/scripts/install.sh), which was
-# later released in X11R6 (xc/config/util/install.sh) with the
-# following copyright and license.
-#
-# Copyright (C) 1994 X Consortium
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to
-# deal in the Software without restriction, including without limitation the
-# rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
-# sell copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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-#
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- eval "$initialize_posix_glob" &&
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- # The rename failed, perhaps because mv can't rename something else
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- }
- } &&
-
- # Now rename the file to the real destination.
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- }
- fi || exit 1
-
- trap '' 0
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-
-# Local variables:
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diff --git a/libs/Makefile.in b/libs/Makefile.in
deleted file mode 100644
index a5cda35..0000000
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+++ /dev/null
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diff --git a/scripts/maf2phy.awk b/scripts/maf2phy.awk
new file mode 100644
index 0000000..3f68e21
--- /dev/null
+++ b/scripts/maf2phy.awk
@@ -0,0 +1,59 @@
+# maf2phy.awk
+# Author: Bernhard Haubold, haubold at evolbio.mpg.de
+# Contributors: Fabian Klötzl, kloetzl at evolbio.mpg.de
+# Date: June 19, 2014
+# Last Modified: February 5, 2015
+BEGIN{
+ if(!n){
+ print "maf2phy.awk: Convert mutation annotation format (maf) as generated by the program mugsy to PHYLIP";
+ print "Usage: awk -f maf2phy.awk -v n=<numberOfTaxa> file.maf > file.phy";
+ exit(-1);
+ }
+ numName = 0;
+ test = "mult=" n;
+}{
+ if(/^a/){
+ if($0 ~ test)
+ open = 1;
+ else
+ open = 0;
+ }
+ if(open && /^s/){
+ if(!s[$2])
+ names[numNames++] = $2;
+ s[$2] = s[$2] $7;
+ }
+}END{
+ # check equal length of sequences
+ len = -1;
+ for(i=0;i<numNames;i++){
+ name = names[i];
+ if(len > 0){
+ if(length(s[name]) != len){
+ print "sequence length should be " len " but is in fact " length(s[name]);
+ exit(-1);
+ }
+ }else
+ len = length(s[name]);
+ }
+ print numNames, len;
+ start = 1;
+ l = 60;
+ for(i=0;i<numNames;i++){
+ name = names[i];
+ printf("%-10.10s",name);
+ print(" " substr(s[name],start,l));
+ }
+ printf("\n");
+ start += l;
+ while(start < len){
+ for(i=0;i<numNames;i++){
+ name = names[i];
+ print(substr(s[name],start,l));
+ }
+ printf("\n");
+ start += l;
+ }
+}
+
+
\ No newline at end of file
diff --git a/scripts/vmatch.sh b/scripts/vmatch.sh
new file mode 100644
index 0000000..cf15c5f
--- /dev/null
+++ b/scripts/vmatch.sh
@@ -0,0 +1,26 @@
+#/usr/bin/bash -f
+# Simulate the anchor distance using vmatch.
+
+# These are all sequences from the ECO29 set.
+SEQS="AE005174.fasta AE005674.fasta AE014073.fasta AE014075.fasta AP009048.fasta AP009240.fasta BA000007.fasta CP000034.fasta CP000036.fasta CP000038.fasta CP000243.fasta CP000247.fasta CP000266.fasta CP000468.fasta CP000800.fasta CP000802.fasta CP000946.fasta CP000948.fasta CP000970.fasta CP001063.fasta CP001396.fasta CP001846.fasta CU928160.fasta CU928161.fasta CU928162.fasta CU928163.fasta CU928164.fasta FM180568.fasta U00096.fasta"
+
+# Loop over all sequences
+for S in $SEQS; do
+ echo $S;
+ Q=${SEQS/$S/}; # All sequences, except S
+
+ # Create the index for S
+ ./mkvtree -db "$S" -dna -allout -pl
+
+ # Recall, that an anchor is unique in S and of some minimum length. Hence
+ # the parameters -mum cand and -l 16. The latter threshold was calculated
+ # by andi.
+
+ # Match all other sequences including their reverse against S
+ ./vmatch -q $Q -mum cand -l 16 -d -p -nodist -noscore -noevalue -noidentity $S > /dev/null
+
+ # In theory we have to calculate the anchors distance here using the previously
+ # computed matches. But since vmatch is already significantly slower than andi,
+ # we skip this step.
+done
+
diff --git a/src/Makefile.in b/src/Makefile.in
deleted file mode 100644
index 616bda1..0000000
--- a/src/Makefile.in
+++ /dev/null
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