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@3417
|
8 years |
Peter |
updating copyright statements
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|
@3415
|
8 years |
Peter |
refs #794
Change logic in configure test looking for libhts/samtools …
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@3413
|
8 years |
Peter |
Prefer variable name HAVE_SAMTOOLS_EXECUTABLE instead of HAVE_SAMTOOLS …
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@3400
|
8 years |
Peter |
refs #794
Deprecate configure option --without-samtools and add new …
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@3381
|
8 years |
Peter |
we require Autoconf 2.64; remove workaround for older Autoconf.
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@3367
|
8 years |
Peter |
update to autoconf-archive-2015-02-04. Note that m4/ax_append_flag.m4 …
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|
|
@3366
|
8 years |
Peter |
prefer private variables in yat.pc. closes #808
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@3365
|
8 years |
Peter |
Use pc from zlib and htslib when linking against those
packages. …
|
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|
@3354
|
8 years |
Peter |
refs #794. fix configure test so it works with htslib.
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|
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@3350
|
8 years |
Peter |
Make configure htslib aware. Header detection changed to look for …
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|
|
@3330
|
8 years |
Peter |
update copyright years
|
|
|
@3306
|
8 years |
Peter |
merge ptach release 0.12.1 into trunk
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|
@3295
|
9 years |
Peter |
merge release 0.12 into trunk
|
|
|
@3250
|
9 years |
Peter |
remove gen_announce.sh.in since creation of announcement is now coded …
|
|
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@3246
|
9 years |
Peter |
move some more targets from Makefile.am to macro YAT_SVN_RELEASE. Make …
|
|
|
@3231
|
9 years |
Peter |
tweak for clarity
|
|
|
@3214
|
9 years |
Peter |
fixes #789. Change behavious of configure so that if INTERNAL_CXXFLAGS …
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|
|
@3201
|
9 years |
Peter |
add #define YAT_HAVE_LIBBAM to API and replace HAVE_LIBBAM accordingly.
|
|
|
@3198
|
9 years |
Peter |
refs #790. Prefer checking (in configure) whether boost work rather …
|
|
|
@3188
|
9 years |
Peter |
merge patch release 0.11.2
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|
|
@3111
|
9 years |
Peter |
refs #737
configure.ac: Define new variables YAT_LIBS, …
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|
|
@3110
|
9 years |
Peter |
Fix test of YAT_LT_LINK_IFELSE. The macro/linking worked also against …
|
|
|
@3091
|
9 years |
Peter |
add test for libz and libbam. refs #737
|
|
|
@3088
|
9 years |
Peter |
avoid repetetive code and add tests for boost libs. refs #737
|
|
|
@3087
|
9 years |
Peter |
refs #737. check if -lgsl is suitable for libtool archive
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|
|
@3086
|
9 years |
Peter |
add a new variable YAT_STATIC_LIBS; perform test if LIBM is suitable …
|
|
|
@3085
|
9 years |
Peter |
fix problem that YAT_CBLAS_LIB were not subtracted from …
|
|
|
@3072
|
9 years |
Peter |
prefer aborting directly when error is detected rather than in the …
|
|
|
@3045
|
10 years |
Peter |
fixes #762. workaround for broken boost header (in v1.41)
|
|
|
@3037
|
10 years |
Peter |
make shell tests work in VPATH build
|
|
|
@3036
|
10 years |
Peter |
common_defs does two things: 1) init test scripts 2) defines some …
|
|
|
@3035
|
10 years |
Peter |
allow test to require 'shared' in shell tests
|
|
|
@3018
|
10 years |
Peter |
merge patch release 0.10.2 into trunk
|
|
|
@2986
|
10 years |
Peter |
merge 0.10-stable branch into trunk
|
|
|
@2981
|
10 years |
Peter |
Skip yat_pc_test.sh when -without-samtools. fixes #748
|
|
|
@2960
|
10 years |
Peter |
merge patch release 0.10.1 into trunk
|
|
|
@2948
|
10 years |
Peter |
prefer AC_SEARCH_LIBS over AC_CHECK_LIB
|
|
|
@2945
|
10 years |
Peter |
avoid warning from Automake
|
|
|
@2943
|
10 years |
Peter |
merge release 0.10 into trunk
|
|
|
@2891
|
10 years |
Peter |
check for samtools in configure; create bam file in 'make check' if we …
|
|
|
@2882
|
10 years |
Peter |
add --enable-assert option (in configure)
|
|
|
@2881
|
10 years |
Peter |
Define PP variables in config.h rather than in CPPFLAGS. Include …
|
|
|
@2878
|
10 years |
Peter |
typo
|
|
|
@2877
|
10 years |
Peter |
prepend LIBS to achieve recommended -lgsl -lcblas -lm
|
|
|
@2876
|
10 years |
Peter |
avoid word enable for something that is turned off with '--without'
|
|
|
@2875
|
10 years |
Peter |
delete leftover comments
|
|
|
@2873
|
10 years |
Peter |
prefer using YAT_MSG_ERROR and simplify computation of …
|
|
|
@2872
|
10 years |
Peter |
prefer YAT_MSG_ERROR. using it in inf test
|
|
|
@2871
|
10 years |
Peter |
prefer YAT_MSG_ERROR. using it in quiet_NAN test
|
|
|
@2869
|
10 years |
Peter |
improve error messages. emove debug code. refs #729
|
|
|
@2868
|
10 years |
Peter |
refs #729. Add configure tests for samtools
|
|
|
@2866
|
10 years |
Peter |
remove -Werror option for automake
|
|
|
@2838
|
10 years |
Peter |
merge release 0.9 into trunk
|
|
|
@2827
|
10 years |
Peter |
Remove -Itop_srcdir from CPPFLAGS. Automake already adds -Isrcdir to …
|
|
|
@2787
|
11 years |
Peter |
update coyright years
|
|
|
@2785
|
11 years |
Peter |
skip boost link tests if --without-boost was provided
|
|
|
@2782
|
11 years |
Jari Häkkinen |
Addresses #714. Added check for boost system libraries. Need to link …
|
|
|
@2781
|
11 years |
Peter |
fix spurious errors in long long test. First, remove -pthread before …
|
|
|
@2780
|
11 years |
Peter |
exclude -pthread from CPPFLAGS if compiler is warning about it. closes #713
|
|
|
@2774
|
11 years |
Peter |
report long long test
|
|
|
@2772
|
11 years |
Peter |
do not ignore BOOST_CPPFLAGS set in AX_BOOST_THREAD
|
|
|
@2769
|
11 years |
Peter |
refs #568. test using multithreaded RNG
|
|
|
@2767
|
11 years |
Peter |
look for boost thread library. refs #568
|
|
|
@2749
|
11 years |
Peter |
add small convenience Makefiles in subdirs. closes #703
|
|
|
@2739
|
11 years |
Peter |
refs #703 using a non-recursive Makefile. Old Makefile.am are kept but …
|
|
|
@2729
|
11 years |
Peter |
Define version on one line in order to avoid that version change in …
|
|
|
@2673
|
11 years |
Peter |
merge release 0.8 into trunk
|
|
|
@2628
|
11 years |
Peter |
avoid aclocal warning
|
|
|
@2627
|
11 years |
Peter |
lippstick for configure output. Avoid prefix 'configure:' and add some …
|
|
|
@2626
|
11 years |
Peter |
fixes #683
|
|
|
@2607
|
11 years |
Peter |
write-protect generated file to avoid editing
|
|
|
@2604
|
11 years |
Peter |
add helper script for release procedure.
|
|
|
@2601
|
11 years |
Peter |
merge release 0.7.3 into trunk. A couple of conflict and needed fix …
|
|
|
@2575
|
11 years |
Peter |
closes #654. support for silent-rules
|
|
|
@2517
|
12 years |
Peter |
use common_defs in documentation_test. Change name to doxygen_test to …
|
|
|
@2487
|
12 years |
Peter |
Change the semantics of htmldir and where htlm docs are
installed. …
|
|
|
@2463
|
12 years |
Peter |
remove deprecated configure options: --with-gsl-prefix and …
|
|
|
@2455
|
12 years |
Peter |
closes #662
|
|
|
@2452
|
12 years |
Peter |
remove test/data/Makefile. distribute small.gff3
|
|
|
@2438
|
12 years |
Peter |
Move yathello test from maintainer-check to installcheck, which means …
|
|
|
@2431
|
12 years |
Peter |
fixes #620. Move version defines from 'version.h' to …
|
|
|
@2418
|
12 years |
Peter |
fixes #655. add a helper script, gen-yat-pc.sh, that generates yat.pc. …
|
|
|
@2354
|
12 years |
Peter |
Before we generate other docs in other formats than html. Remove …
|
|
|
@2341
|
12 years |
Peter |
New namespace omic and new class omic::DNA. closes #377
|
|
|
@2326
|
12 years |
Peter |
update boost m4 macro, which now uses …
|
|
|
@2309
|
12 years |
Peter |
create dummie doxygen.mk only if it doesnt exist
|
|
|
@2308
|
12 years |
Peter |
creating dummie doxygen.mk during configure. fixes #636
|
|
|
@2300
|
13 years |
Peter |
update BUG_REPORT
|
|
|
@2297
|
13 years |
Peter |
dvi, ps, and pdf docs are no longer supported
|
|
|
@2266
|
13 years |
Peter |
use 'echo' rather than the variable ECHO decided by libtool. The …
|
|
|
@2264
|
13 years |
Peter |
prefer hard-coding name yat because it increases readability and is …
|
|
|
@2244
|
13 years |
Peter |
fixes #619
|
|
|
@2241
|
13 years |
Peter |
remove AC_PROG_INSTALL which is already called by AM_INIT_AUTOMAKE and …
|
|
|
@2228
|
13 years |
Peter |
Using the parallel-tests driver. All tests are now by default verbose, …
|
|
|
@2227
|
13 years |
Peter |
automake 1.11 is now required. refs #475
|
|
|
@2224
|
13 years |
Peter |
Lift out rule generating doxygen.mk into one common place …
|
|
|
@2222
|
13 years |
Peter |
prefer yat (lower case)
|
|
|
@2161
|
13 years |
Peter |
updating copyright years
|
|
|
@2153
|
13 years |
Peter |
refs #603. Boost 1.35 is now required
|
|
|
@2131
|
13 years |
Peter |
prefer using AC_CONFIG_HEADERS rather than AC_CONFIG_HEADER
|
|
|