Commit d271e86f authored by Sascha Steinbiss's avatar Sascha Steinbiss
Browse files

New upstream version 1.6.0+ds

parent 17a2684e

.travis.yml

+3 −3
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@@ -42,13 +42,13 @@ matrix: 
      env: opt=no cairo=no

    - os: osx

      compiler: gcc

      env: default=yes

      env: default=yes PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"

    - os: osx

      compiler: gcc

      env: assert=no

      env: assert=no PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"

    - os: osx

      compiler: gcc

      env: amalgamation=yes

      env: amalgamation=yes PKG_CONFIG_PATH="/usr/local/opt/libffi/lib/pkgconfig"

    - os: linux

      compiler: gcc

      env: opt=no cairo=no

CHANGELOG

+6 −0
Original line number Diff line number Diff line 
changes in version 1.6.0 (2020-01-06)



- improve error handling in some tools

- C API has been extended significantly





changes in version 1.5.10 (2017-08-04)



- bugfixes and cleanups

CONTRIBUTORS

+1 −1
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@@ -11,5 +11,5 @@ gordon@gremme.org I left someone out or missed something. 
- Brent Pedersen (python bindings, patches)

- Christin Schaerfer (AnnotationSketch, sketch tool)

- David Schmitz-Huebsch (mgth/ subdirectory, mgth tool)

- Dirk Willrodt (genomediff tool, SAM/BAM, patches)

- Dirk Willrodt (genomediff, condenseq tool, SAM/BAM, wavelet tree, patches)

- Daniel Standage (GtSetSourceVisitor, GtFeatureInStream, python bindings, patches)

INSTALL

+25 −2
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@@ -101,8 +101,31 @@ preferred option. 
Use the 'useshared=yes' make option to ignore the embedded code copies in the

GenomeTools source distribution and to use the system-wide versions. The following

libraries (and their development headers) are required to be present:

zlib, bzlib2, liblua5.1, lua-filesystem, lua-lpeg, lua-md5, libexpat, libtre,

libcairo + libpango (only unless 'cairo=no' is used), libsqlite3 and libbam.



 - zlib (https://zlib.net/)

   Debian/Ubuntu: zlib1g-dev

 - bzlib2 (https://www.sourceware.org/bzip2/)

   Debian/Ubuntu: libbz2-dev

 - liblua5.1 (https://www.lua.org/)

   Debian/Ubuntu: liblua5.1-0-dev

 - lua-filesystem (https://keplerproject.github.io/luafilesystem/)

   Debian/Ubuntu: lua-filesystem-dev

 - lua-lpeg (http://www.inf.puc-rio.br/~roberto/lpeg/)

   Debian/Ubuntu: lua-lpeg-dev

 - lua-md5 (https://keplerproject.github.io/md5/)

   Debian/Ubuntu: lua-md5-dev

 - libexpat (https://github.com/libexpat/libexpat)

   Debian/Ubuntu: libexpat1-dev

 - libtre (https://github.com/laurikari/tre/)

   Debian/Ubuntu: libtre-dev

 - libcairo (only unless 'cairo=no' is used) (https://cairographics.org/)

   Debian/Ubuntu: libcairo2-dev

 - libpango (only unless 'cairo=no' is used) (https://www.pango.org/)

   Debian/Ubuntu: libpango1.0-dev

 - libsqlite3 (https://www.sqlite.org/)

   Debian/Ubuntu: libsqlite3-dev

 - libbam (http://www.htslib.org/)

   Debian/Ubuntu: libbam-dev





Testing GenomeTools (optional)

Makefile

+1 −1
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@@ -400,7 +400,6 @@ LIBGENOMETOOLS_DIRS:= src/core \ 
                      src/extended \

                      src/gtlua \

                      src/match \

                      src/gth \

                      src/ltr \

                      src/mgth
@@ -495,6 +494,7 @@ ifeq ($(amalgamation),yes) 
  LIBGENOMETOOLS_PRESRC:=$(filter-out $(SQLITE3_SRC),\

                         $(LIBGENOMETOOLS_PRESRC))

  LIBGENOMETOOLS_SRC:=obj/amalgamation.c

  GT_CFLAGS+=-Wno-strict-overflow

else

  LIBGENOMETOOLS_SRC:=$(LIBGENOMETOOLS_PRESRC)

endif