GenMap 1.2.0 release

cpockrandt · Feb 21, 2020 · 9857e0d · 9857e0d
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,6 +1,24 @@
 Changelog
 ^^^^^^^^^
 
+1.2.0 (2020-02-21)
+""""""""""""""""""
+
+Features
+--------
+
+* **BREAKING CHANGE!** k-mers are searched on both strands by default. Can be turned off with ``--no-reverse-complement``
+* bedgraph output (``*.bg``) replaces bed output (``*.bed``) (bed output is still supported with ``--bed`` but deprecated and removed from the help string)
+* allow user to specify a filename with ``--output`` if only a single fasta file has been indexed (previously only the directory could be specified)
+
+Fixes
+-----
+
+* truncate fasta identifiers after first space
+* allow indexing fasta files with ``*.fas`` filename ending
+* runtime speedup when BED file is provided for computation on a subset of the input (``--selection``)
+* reduced progress output on terminal when processing multiple fasta files
+
 1.1.0 (2019-11-17)
 """"""""""""""""""
 
@@ -11,7 +29,7 @@ Changelog
 1.0.2 (2019-09-04)
 """"""""""""""""""
 
-* BED output format fixed (end position was off by one, i.e. closed interval instead of half-closed interval) 
+* BED output format fixed (end position was off by one, i.e. closed interval instead of half-closed interval)
 
 1.0.1 (2019-06-11)
 """"""""""""""""""

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -18,7 +18,7 @@ project (genmap CXX)
 
 # change this after every release
 set (SEQAN_APP_VERSION_MAJOR "1")
-set (SEQAN_APP_VERSION_MINOR "1")
+set (SEQAN_APP_VERSION_MINOR "2")
 set (SEQAN_APP_VERSION_PATCH "0")
 # don't change the following
 set (SEQAN_APP_VERSION "${SEQAN_APP_VERSION_MAJOR}.${SEQAN_APP_VERSION_MINOR}.${SEQAN_APP_VERSION_PATCH}")

diff --git a/README.rst b/README.rst
@@ -77,13 +77,13 @@ To verify whether your CPU supports these instructions sets you can check the ou
 |   :height: 60px                 | `Mac 64 bit optimized`_   | |VERSION| (|BUILD_DATE|) | requires SSE4               |
 +---------------------------------+---------------------------+--------------------------+-----------------------------+
 
-.. _Linux 64 bit: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.1.0/genmap-1.1.0-Linux-x86_64.zip
-.. _Linux 64 bit optimized: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.1.0/genmap-1.1.0-Linux-x86_64-sse4.zip
-.. _Mac 64 bit: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.1.0/genmap-1.1.0-Darwin-x86_64.zip
-.. _Mac 64 bit optimized: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.1.0/genmap-1.1.0-Darwin-x86_64-sse4.zip
+.. _Linux 64 bit: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.2.0/genmap-1.2.0-Linux-x86_64.zip
+.. _Linux 64 bit optimized: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.2.0/genmap-1.2.0-Linux-x86_64-sse4.zip
+.. _Mac 64 bit: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.2.0/genmap-1.2.0-Darwin-x86_64.zip
+.. _Mac 64 bit optimized: https://github.com/cpockrandt/genmap/releases/download/genmap-v1.2.0/genmap-1.2.0-Darwin-x86_64-sse4.zip
 
-.. |VERSION| replace:: 1.1.0
-.. |BUILD_DATE| replace:: 2019-11-17
+.. |VERSION| replace:: 1.2.0
+.. |BUILD_DATE| replace:: 2020-02-21
 
 Building from source
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