- use factory classes exclusively in bamcollate2

- add setup for irods stream handlers in bamtofastq and bamcollate2
gt1 · Jan 21, 2015 · 2fd027d · 2fd027d
1 parent 8d4fac4
commit 2fd027d
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Showing 4 changed files with 88 additions and 115 deletions.
diff --git a/configure.ac b/configure.ac
@@ -187,7 +187,7 @@ if test "${have_libmaus}" = "no" ; then
 fi
 
 AC_LANG_PUSH([C++])
-AC_MSG_CHECKING([whether we libmaus has support for io_lib])
+AC_MSG_CHECKING([whether libmaus has support for io_lib])
 	AC_LINK_IFELSE([AC_LANG_SOURCE([
 #include <libmaus/LibMausConfig.hpp>
 
@@ -208,6 +208,57 @@ if test "${have_libmaus_iolib}" = "yes" ; then
 	LIBMAUSIOLIBDEFINE="#define BIOBAMBAM_LIBMAUS_HAVE_IO_LIB"
 fi
 
+## zzzz
+
+AC_LANG_PUSH([C++])
+AC_MSG_CHECKING([whether libmaus has support for iRODS])
+	AC_LINK_IFELSE([AC_LANG_SOURCE([
+#include <libmaus/LibMausConfig.hpp>
+
+				int main(int argc, char * argv[[]]) {
+					#if ! defined(LIBMAUS_HAVE_IRODS)
+					#error "installed libmaus does not support iRODS"
+					#endif
+					return 0;
+			}])],
+			have_libmaus_irods=yes,
+			have_libmaus_irods=no
+		)
+AC_LANG_POP
+AC_MSG_RESULT($have_libmaus_irods)
+
+LIBMAUSIRODSDEFINE=
+LIBMAUSIRODSCPPFLAGS=
+LIBMAUSIRODSLIBS=
+if test "${have_libmaus_irods}" = "yes" ; then
+	if test ! -z "${with_libmaus}" ; then
+		PKGCONFIGPATHSAVE="${PKG_CONFIG_PATH}"
+		if test -z "${PKG_CONFIG_PATH}" ; then
+			export PKG_CONFIG_PATH="${with_libmaus}/lib/pkgconfig"
+		else
+			export PKG_CONFIG_PATH="${with_libmaus}/lib/pkgconfig:${PKG_CONFIG_PATH}"
+		fi
+	fi
+
+	PKG_CHECK_MODULES([libmausirods],[libmausirods >= 0.0.187])
+
+	LIBMAUSIRODSCPPFLAGS="${libmausirods_CFLAGS}"
+	LIBMAUSIRODSLIBS="${libmausirods_LIBS}"
+
+	LIBMAUSCPPFLAGS="${LIBMAUSCPPFLAGS} ${LIBMAUSIRODSCPPFLAGS}"
+	LIBMAUSLIBS="${LIBMAUSLIBS} ${LIBMAUSIRODSLIBS}"
+	CPPFLAGS="${CPPFLAGS} ${LIBMAUSIRODSCPPFLAGS}"
+	LIBS="${LIBS} ${LIBMAUSIRODSLIBS}"
+
+	if test ! -z "${with_libmaus}" ; then
+		if test ! -z "${PKGCONFIGPATHSAVE}" ; then
+			export PKG_CONFIG_PATH="${PKGCONFIGPATHSAVE}"
+		fi
+	fi
+
+	LIBMAUSIRODSDEFINE="#define BIOBAMBAM_LIBMAUS_HAVE_IRODS"
+fi
+
 CPPFLAGS="${CPPFLAGS_SAVE}"
 LDFLAGS="${LDFLAGS_SAVE}"
 LIBS="${LIBS_SAVE}"
@@ -357,6 +408,7 @@ AC_SUBST([LIBMAUSCPPFLAGS])
 AC_SUBST([LIBMAUSLIBS])
 # 
 AC_SUBST([LIBMAUSIOLIBDEFINE])
+AC_SUBST([LIBMAUSIRODSDEFINE])
 #
 AC_SUBST([LIFTINGWAVELETTRANSFORMDEFINE])
 AC_SUBST([BAMREFDEPTHPEAKS])

diff --git a/src/biobambam/BamBamConfig.hpp.in b/src/biobambam/BamBamConfig.hpp.in
@@ -22,5 +22,6 @@
 @LIBMAUSIOLIBDEFINE@
 @BIOBAMBAM_HAVE_XERCES_C@
 @BIOBAMBAM_HAVE_GMP@
+@LIBMAUSIRODSDEFINE@
 
 #endif
diff --git a/src/programs/bamcollate2.cpp b/src/programs/bamcollate2.cpp
@@ -1008,67 +1008,19 @@ void bamcollate2CollatingRanking(libmaus::util::ArgInfo const & arginfo)
 	libmaus::util::TempFileRemovalContainer::addTempFile(tmpfilename);
 	std::string const inputformat = arginfo.getValue<std::string>("inputformat",getDefaultInputFormat());
 	std::string const inputfilename = arginfo.getValue<std::string>("filename","-");
-	uint64_t const numthreads = arginfo.getValue<uint64_t>("threads",0);
 
 	unsigned int const hlog = arginfo.getValue<unsigned int>("colhlog",18);
 	uint64_t const sbs = arginfo.getValueUnsignedNumeric<uint64_t>("colsbs",128ull*1024ull*1024ull);
 
-	if ( inputformat == "bam" )
-	{
-		BamToFastQInputFileStream bamin(inputfilename);
-
-		if ( numthreads > 0 )
-		{
-			libmaus::bambam::BamParallelCircularHashCollatingBamDecoder CHCBD(
-				bamin.in,
-				numthreads,
-				tmpfilename,excludeflags,
-				true, /* put rank */
-				hlog,
-				sbs
-				);
-			bamcollate2CollatingRanking(arginfo,CHCBD);
-		}
-		else
-		{
-			libmaus::bambam::BamCircularHashCollatingBamDecoder CHCBD(
-				bamin.in,
-				tmpfilename,excludeflags,
-				true, /* put rank */
-				hlog,
-				sbs
-				);
-			bamcollate2CollatingRanking(arginfo,CHCBD);
-		}
-	}
-	#if defined(BIOBAMBAM_LIBMAUS_HAVE_IO_LIB)
-	else if ( inputformat == "sam" )
-	{
-		libmaus::bambam::ScramCircularHashCollatingBamDecoder CHCBD(inputfilename,"r","",
-			tmpfilename,excludeflags,
-			true, /* put rank */
-			hlog,sbs
-		);
-		bamcollate2CollatingRanking(arginfo,CHCBD);
-	}
-	else if ( inputformat == "cram" )
-	{
-		std::string const reference = arginfo.getValue<std::string>("reference","");
-		libmaus::bambam::ScramCircularHashCollatingBamDecoder CHCBD(inputfilename,"rc",reference,
-			tmpfilename,excludeflags,
-			true, /* put rank */
-			hlog,sbs
-		);
-		bamcollate2CollatingRanking(arginfo,CHCBD);
-	}
-	#endif
-	else
-	{
-		libmaus::exception::LibMausException se;
-		se.getStream() << "unknown input format " << inputformat << std::endl;
-		se.finish();
-		throw se;
-	}
+	uint64_t const inputbuffersize = arginfo.getValueUnsignedNumeric<uint64_t>("inputbuffersize",getDefaultInputBufferSize());
+	libmaus::aio::PosixFdInputStream PFIS(STDIN_FILENO,inputbuffersize);
+	libmaus::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
+		libmaus::bambam::BamMultiAlignmentDecoderFactory::construct(
+			arginfo,true /* put rank */, 0 /* copy stream */, PFIS
+		)
+	);
+	libmaus::bambam::CircularHashCollatingBamDecoder CHCBD(decwrapper->getDecoder(),tmpfilename,excludeflags,hlog,sbs);
+	bamcollate2CollatingRanking(arginfo,CHCBD);
 
 	std::cout.flush();
 }
@@ -1383,67 +1335,19 @@ void bamcollate2CollatingPostRanking(libmaus::util::ArgInfo const & arginfo)
 	libmaus::util::TempFileRemovalContainer::addTempFile(tmpfilename);
 	std::string const inputformat = arginfo.getValue<std::string>("inputformat",getDefaultInputFormat());
 	std::string const inputfilename = arginfo.getValue<std::string>("filename","-");
-	uint64_t const numthreads = arginfo.getValue<uint64_t>("threads",0);
 
 	unsigned int const hlog = arginfo.getValue<unsigned int>("colhlog",18);
 	uint64_t const sbs = arginfo.getValueUnsignedNumeric<uint64_t>("colsbs",128ull*1024ull*1024ull);
 
-	if ( inputformat == "bam" )
-	{
-		BamToFastQInputFileStream bamin(inputfilename);
-
-		if ( numthreads > 0 )
-		{
-			libmaus::bambam::BamParallelCircularHashCollatingBamDecoder CHCBD(
-				bamin.in,
-				numthreads,
-				tmpfilename,excludeflags,
-				true, /* put rank */
-				hlog,
-				sbs
-				);
-			bamcollate2CollatingPostRanking(arginfo,CHCBD);
-		}
-		else
-		{
-			libmaus::bambam::BamCircularHashCollatingBamDecoder CHCBD(
-				bamin.in,
-				tmpfilename,excludeflags,
-				true, /* put rank */
-				hlog,
-				sbs
-				);
-			bamcollate2CollatingPostRanking(arginfo,CHCBD);
-		}
-	}
-	#if defined(BIOBAMBAM_LIBMAUS_HAVE_IO_LIB)
-	else if ( inputformat == "sam" )
-	{
-		libmaus::bambam::ScramCircularHashCollatingBamDecoder CHCBD(inputfilename,"r","",
-			tmpfilename,excludeflags,
-			true, /* put rank */
-			hlog,sbs
-		);
-		bamcollate2CollatingPostRanking(arginfo,CHCBD);
-	}
-	else if ( inputformat == "cram" )
-	{
-		std::string const reference = arginfo.getValue<std::string>("reference","");
-		libmaus::bambam::ScramCircularHashCollatingBamDecoder CHCBD(inputfilename,"rc",reference,
-			tmpfilename,excludeflags,
-			true, /* put rank */
-			hlog,sbs
-		);
-		bamcollate2CollatingPostRanking(arginfo,CHCBD);
-	}
-	#endif
-	else
-	{
-		libmaus::exception::LibMausException se;
-		se.getStream() << "unknown input format " << inputformat << std::endl;
-		se.finish();
-		throw se;
-	}
+	uint64_t const inputbuffersize = arginfo.getValueUnsignedNumeric<uint64_t>("inputbuffersize",getDefaultInputBufferSize());
+	libmaus::aio::PosixFdInputStream PFIS(STDIN_FILENO,inputbuffersize);
+	libmaus::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
+		libmaus::bambam::BamMultiAlignmentDecoderFactory::construct(
+			arginfo,true /* put rank */, 0 /* copy stream */, PFIS
+		)
+	);
+	libmaus::bambam::CircularHashCollatingBamDecoder CHCBD(decwrapper->getDecoder(),tmpfilename,excludeflags,hlog,sbs);
+	bamcollate2CollatingPostRanking(arginfo,CHCBD);
 
 	std::cout.flush();
 }
@@ -1502,10 +1406,18 @@ void bamcollate2(libmaus::util::ArgInfo const & arginfo)
 	}
 }
 
+#if defined(LIBMAUS_HAVE_IRODS)
+#include <libmaus/irods/IRodsInputStreamFactory.hpp>
+#endif
+
 int main(int argc, char * argv[])
 {
 	try
 	{
+		#if defined(LIBMAUS_HAVE_IRODS)
+                libmaus::irods::IRodsInputStreamFactory::registerHandler();
+                #endif
+
 		libmaus::timing::RealTimeClock rtc; rtc.start();
 
 		::libmaus::util::ArgInfo arginfo(argc,argv);

diff --git a/src/programs/bamtofastq.cpp b/src/programs/bamtofastq.cpp
@@ -1041,10 +1041,18 @@ void bamtofastq(libmaus::util::ArgInfo const & arginfo)
 	}
 }
 
+#if defined(LIBMAUS_HAVE_IRODS)
+#include <libmaus/irods/IRodsInputStreamFactory.hpp>
+#endif
+
 int main(int argc, char * argv[])
 {
 	try
 	{
+		#if defined(LIBMAUS_HAVE_IRODS)
+		libmaus::irods::IRodsInputStreamFactory::registerHandler();
+		#endif
+
 		libmaus::timing::RealTimeClock rtc; rtc.start();
 
 		::libmaus::util::ArgInfo arginfo(argc,argv);