New upstream version 2.0.0+dfsg

--------------

You may use Subread package by directly downloading a binary release suitable for your operating system (no compilation is needed), or you may build it from the source. Here we describe how to install it from the source.

Download the latest version of Subread package from http://subread.sourceforge.net/. The source release includes a keyword 'source' in the name of the tar ball. Uncompress the tar ball, enter the 'src' directory and issue the following command to build it for Linux OS :

Download the latest version of Subread package from http://subread.sourceforge.net/. The source release includes a keyword 'source' in the name of the tar ball. Uncompress the tar ball, enter the 'src' directory and issue one of the following commands to build it.

*** for Linux OS, use command:

make -f Makefile.Linux

For Mac OS, use command:

*** For Windows, use command:

make -f Makefile.Windows

You need to have ``gcc" and ``make" in %PATH% to build the Windows-version of Subread. It is recommended to download and install Mingw-w64 before building Subread, for that Mingw-w64 contains all the necessary prorgams and libraries.

If you have had Mingw-w64 installed, you should use this command: 

mingw32-make -f Makefile.Windows

Still, you need to make sure that mingw_64/bin, which contains mingw32-make.exe and gcc.exe, is in %PATH%. We strongly recommend to build the 64-bit version Subread programs (by using the 64-bit Mingw package) because the 32-bit version Subread programs have very limited memory access.

*** For Mac OS, use command:

make -f Makefile.MacOS

For FreeBSD OS, use command:

*** For FreeBSD OS, use command:

gmake -f Makefile.FreeBSD

\begin{center}

{\Huge\bf Rsubread/Subread Users Guide}\\

\vspace{1 cm}

{\centering\large Rsubread v1.34.6/Subread v1.6.5\\}

{\centering\large Rsubread v2.0.0/Subread v2.0.0\\}

\vspace{1 cm}

\centering 18 July 2019\\

\centering 2 September 2019\\

\vspace{5 cm}

\Large Wei Shi and Yang Liao\\

\vspace{1 cm}

If you use {\Rsubread}, you can cite:

\begin{quote}

Liao Y, Smyth GK and Shi W (2019). The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. \emph{Nucleic Acids Research}, doi: 10.1093/nar/gkz114. [Epub ahead of print].

Liao Y, Smyth GK and Shi W (2019). 

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. 

\emph{Nucleic Acids Research}, 47(8):e47.

\\

{\color{blue}{\url{http://www.ncbi.nlm.nih.gov/pubmed/30783653}} }

\end{quote}

If you use \featureCounts, you can cite:

\begin{quote}

Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. \emph{Bioinformatics}, 30(7):923-30.

Liao Y, Smyth GK and Shi W (2014). 

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. 

\emph{Bioinformatics}, 30(7):923-30.

\\

{\color{blue}{\url{http://www.ncbi.nlm.nih.gov/pubmed/24227677}}}

\end{quote}

If you use {\Subread} or {\Subjunc} aligners, you can cite:

\begin{quote}

Liao Y, Smyth GK and Shi W (2013). The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. \emph{Nucleic Acids Research}, 41(10):e108.

Liao Y, Smyth GK and Shi W (2013). 

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. 

\emph{Nucleic Acids Research}, 41(10):e108.

\\

{\color{blue}{\url{http://www.ncbi.nlm.nih.gov/pubmed/23558742}} }

\end{quote}

\newpage

\section{Download and installation}

BiocManager::install("Rsubread")

\end{Rcode}

Alternatively, you may download the {\Rsubread} source package directly from {\color{blue}{\url{http://bioconductor.org/packages/release/bioc/html/Rsubread.html}} } and install it from source.\\

To install {\Rsubread} on a Windows computer, the R software has to be launched from Linux Bash Shell (Windows 10) or a unix-like environment such as cygwin.

Alternatively you may download it from {\Rsubread} web page {\color{blue}{\url{http://bioconductor.org/packages/release/bioc/html/Rsubread.html}}} and install it manually.

\subsection{Install SourceForge {\Subread} package}

\subsubsection{Installation from a binary distribution}

\subsubsection{Install from a binary distribution}

This is the easiest way to install the SourceForge {\Subread} package.

Binary distributions can be downloaded for Linux and Mac OS X from {\color{blue}{\url{http://subread.sourceforge.net}}}.

The Linux binary distribution can be run on multiple variants of Linux including Debian, Ubuntu, Fedora and Cent OS.

Binary distributions are available for Linux, Macintosh and Windows operating systems and they can be downloaded from {\color{blue}{\url{http://subread.sourceforge.net}}}.

The Linux binary distribution can be run on multiple Linux variants including Debian, Ubuntu, Fedora and Cent OS.

For Windows 10, the Linux binary distribution can be directly installed on the Linux Bash Shell. 

If a unix-like environment such as cygwin is installed on a Windows computer, the Linux binary distribution can also be installed in that environment.

To install {\Subread} package on FreeBSD or Solaris, you will have to install from source.

To install {\Subread} package on FreeBSD or Solaris, you will have to install them for source.

\subsubsection{Installation from the source package}

\subsubsection{Install from source on a Unix or Macintosh computer}

Download {\Subread} source package to your working directory from SourceForge \\

{\color{blue}{\url{http://subread.sourceforge.net}}}, and type the following command to uncompress it:\\

\code{make -f Makefile.SunOS}\\

If you use a Windows computer, you can install it on the Linux Bash Shell (Windows 10) or install it on a unix-like environment such as cygwin.

The command for installation is the same as that for the installation on a Linux operating system.\\

A new directory called \code{bin} will be created under the home directory of the software package, and the executables generated from the compilation are saved to that directory.

To enable easy access to these executables, you may copy them to a system directory such as \code{/usr/bin} or add the path to them to your search path (your search path is usually specified in the environment variable \code{`PATH'}).

\subsubsection{Install from source on a Windows computer}

The MinGW software tool  (http://www.mingw.org/) needs to installed to compile Subread.

\section{How to get help}

#include <sys/ioctl.h>

#include <netinet/in.h>

#include <net/if.h>

#include <sys/sysinfo.h>

#endif

#include <sys/types.h>

#include <sys/sysinfo.h>

#endif

	char * ret = lname;

	int x1;

	for(x1 = strlen(lname)-1; x1>=0; x1--){

		if(lname [x1] == '/'){

	for(x1 = strlen(lname)-2; x1>=0; x1--){

		if(lname [x1] == '/'||lname [x1] == '\\'){

			ret = lname + x1 + 1;

			break;

		}

	HashTableDestroy( tab -> contig_table );

}

int read_contig_fasta(fasta_contigs_t * tab, char * fname){

	FILE * fp = f_subr_open(fname, "r");

	if(fp != NULL){

	autozip_fp fp;

	int rv = autozip_open(fname, &fp);

	if(rv>=0){

		tab -> contig_table = HashTableCreate(3943);

		tab -> size_table = HashTableCreate(3943);

		chro_name[0]=0;

		while(1){

			char nch = fgetc(fp);

			int nch = autozip_getch(&fp);

			if(nch<0)break;

			if(status == 0){

				assert(nch == '>');

				status = 1;

						unsigned int new_bin_space = current_bin_space / 4 * 5;

						if(current_bin_space > 0xffff0000 /5 * 4){

							assert(0);

							return 1;

						}

						bin_block = realloc(bin_block, new_bin_space);

						memset(bin_block + current_bin_space, 0, new_bin_space - current_bin_space);

			}

		}

		fclose(fp);

		autozip_close(&fp);

		return 0;

	}

	return 1;

	for(x=0;x<16;x++){

		SUBREADprintf("%02X", md5v[x]);

	}

	#ifdef __MINGW32__

	SUBREADprintf("\t'%s'\t%016I64X\t%I64u\t%.9f\n", s, randv, randv, randv*1./0xffffffffffffffffllu);

	#else

	SUBREADprintf("\t'%s'\t%016llX\t%llu\t%.9f\n", s, randv, randv, randv*1./0xffffffffffffffffllu);

	#endif

}

//#define TESTHelpermain main

#endif

#ifdef __MINGW32__

#include <windows.h>

#endif

int get_free_total_mem(size_t * total, size_t * free_mem){

#ifdef FREEBSD

    return -1;

#endif

#ifdef __MINGW32__

	MEMORYSTATUSEX statex;

	statex.dwLength = sizeof (statex);

	GlobalMemoryStatusEx (&statex);

	(*total) = statex.ullTotalPhys;

	(*free_mem) = statex.ullAvailPhys;

	return 0;

#else

#ifdef MACOS

    mach_msg_type_number_t count = HOST_VM_INFO_COUNT;

    vm_statistics_data_t vmstat;

    *total = sinf.totalram;

    return 0;

#endif

#endif

}

	@echo "  Subread currently supports Linux, Mac OS X and FreeBSD. Please choose the correct Makefile to build Subread."

	@echo 

	@echo "  For building subread in Linux, please run ' make -f Makefile.Linux '."

	@echo "  For building subread in Windows, please run ' make -f Makefile.Windows '. See README.txt for how to find the necessary programs and libraries."

	@echo "  For building subread in Mac OS X, please run ' make -f Makefile.MacOS '."

	@echo "  For building subread in FreeBSD, please run ' gmake -f Makefile.FreeBSD '."

	@echo

CC = gcc ${CCFLAGS} ${STATIC_MAKE} -ggdb -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 

ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge core-bigtable seek-zlib

ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge core-bigtable seek-zlib input-blc

ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS})

ALL_H=$(addsuffix .h, ${ALL_LIBS})

ALL_C=$(addsuffix .c, ${ALL_LIBS})