Merge pull request #10 from pachterlab/devel

Devel

Author: Yenaled

.gitignore

@@ -7,6 +7,9 @@ ext/zlib-ng/src/
 ext/zlib-ng/build/
 ext/zlib-ng/tmp/
 
+ext/htslib/tmp/
+ext/htslib/src/
+
 *.pyc
 
 CMakeCache.txt
@@ -19,3 +22,4 @@ CTestTestfile.cmake
 debug/
 release/
 .snakemake
+src/.Rhistory

CMakeLists.txt

@@ -25,9 +25,15 @@ ELSE(LINK MATCHES shared)
     message("shared build")
 ENDIF(LINK MATCHES static)
 
+set(USE_HTSLIB "ON")
+if (NO_HTSLIB)
+    set(USE_HTSLIB OFF)
+endif()
+
 if(EMSCRIPTEN_BUILD)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -s USE_ZLIB=1")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -s USE_ZLIB=1")
+    set(USE_HTSLIB OFF)
 endif()
 
 add_subdirectory(src)
@@ -55,3 +61,21 @@ if (ZLIBNG)
     )
 endif(ZLIBNG)
 
+if (USE_HTSLIB)
+    message("using htslib")
+    ExternalProject_Add(htslib
+    PREFIX ${PROJECT_SOURCE_DIR}/ext/htslib
+    SOURCE_DIR ${PROJECT_SOURCE_DIR}/ext/htslib
+    BUILD_IN_SOURCE 1
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND make lib-static
+    INSTALL_COMMAND ""
+    )
+else()
+    set(NO_HTSLIB "ON")
+    add_compile_definitions("NO_HTSLIB=ON")
+    message("not using htslib")
+endif()
+
+
+

ext/htslib/.gitignore

@@ -0,0 +1,21 @@
+*.o
+*.pico
+/version.h
+
+lib*.a
+lib*.dylib
+lib*.so
+lib*.so.*
+
+/bgzip
+/tabix
+/test/fieldarith
+/test/hfile
+/test/sam
+/test/test-vcf-api
+/test/test-vcf-sweep
+/test/test_view
+/test/*.tmp
+/test/*.tmp.*
+
+/TAGS

ext/htslib/.travis.yml

@@ -0,0 +1,8 @@
+# Control file for continuous integration testing at http://travis-ci.org/
+
+language: c
+compiler:
+  - clang
+  - gcc
+
+script: make -e && make test

ext/htslib/README.md

@@ -0,0 +1,17 @@
+HTSlib is an implementation of a unified C library for accessing common file
+formats, such as [SAM, CRAM and VCF][1], used for high-throughput sequencing
+data, and is the core library used by [samtools][2] and [bcftools][3].
+HTSlib only depends on [zlib][4].
+It is known to be compatible with gcc, g++ and clang.
+
+HTSlib implements a generalized BAM index, with file extension `.csi`
+(coordinate-sorted index). The HTSlib file reader first looks for the new index
+and then for the old if the new index is absent.
+
+This project also includes the popular tabix indexer, which indexes both `.tbi`
+and `.csi` formats, and the bgzip compression utility.
+
+[1]: http://samtools.github.io/hts-specs/
+[2]: http://samtools.github.io/bcftools/
+[3]: http://github.com/samtools/samtools
+[4]: http://zlib.net/