[med-svn] [Git][med-team/subread][upstream] New upstream version 2.0.3+dfsg
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Mon Jul 19 18:33:42 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / subread
Commits:
688c6999 by Nilesh Patra at 2021-07-19T22:51:22+05:30
New upstream version 2.0.3+dfsg
- - - - -
3 changed files:
- README.txt
- src/makefile.version
- src/readSummary.c
Changes:
=====================================
README.txt
=====================================
@@ -1,8 +1,8 @@
Installation
--------------
-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.
+You may use Subread package by directly downloading a binary release suitable for your operating system (no compilation is required), or by installing it to your computer 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 one of the following commands to build it.
+Here we describe how to install it from the source. You will need to download the source release of the 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:
@@ -12,13 +12,12 @@ make -f Makefile.Linux
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.
+When building Subread on a Windows computer, the ``gcc" and ``make" programs will be used. The paths to these two programs need to be included in your environment variable PATH so that these two programs can be accessed.
-If you have had Mingw-w64 installed, you should use this command:
+An alternative way to build Subread on a Windows computer is to use Mingw-w64. This is often a more reliable approach. After installing Mingw-w64, you can just use the following command to build Subread. Note that the path to the two mingw_64 executables ``mingw32-make.exe" and ``gcc.exe" should also be included in your environment variable PATH.
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:
@@ -28,56 +27,17 @@ make -f Makefile.MacOS
gmake -f Makefile.FreeBSD
-If the build is successful, a new directory called 'bin' will be created under the home directory of the package (ie. one level up from 'src' directory). The 'bin directory contains all the generated executables. To enable easy access to these executables, you may copy the executables to a system directory such as '/usr/bin' or add the path to the executables to your search path (add path to your environment variable `PATH').
+If the build is successful, a new directory called 'bin' will be created under the home directory of the package (ie. one level up from 'src' directory). The 'bin directory contains all the generated executables. To enable easy access to these executables, you may copy the executables to a system directory such as '/usr/bin' or add the path to the executables to your search paths that are usually stored in your environment variable PATH.
Content
--------------
-annotation Directory including NCBI RefSeq gene annotations for genomes 'hg19', 'hg38', 'mm10' and 'mm9'.
- Each row is an exon. Entrez gene identifiers and chromosomal coordinates are provided for each exon.
-bin Directory including executables after compilation (or directly available from a binary release).
-doc Directory including the users manual.
-LICENSE The license agreement for using this package.
-README.txt This file.
-src Directory including source code (binary releases do not have this directory).
-test Directory including test data and scripts.
-
-A Quick Start
---------------
-Build index for a reference genome:
-
- subread-buildindex -o my_index chr1.fa chr2.fa ...
- (You may provide a single FASTA file including all chromosomal sequences).
-
-Align a single-end RNA-seq dataset to the reference genome:
-
- subread-align -i my_index -r reads.txt -t 0 -o subread_results.bam
-
-Align a paired-end genomic DNA-seq dataset to the reference genome:
-
- subread-align -i my_index -r reads1.txt -R reads2.txt -t 1 -o subread_results_PE.bam
-
-Detect exon-exon junctions from a paired-end RNA-seq dataset (read mapping results are also produced):
-
- subjunc -i my_index -r reads1.txt -R reads2.txt -o subjunc_results.bam
-
-Assign mapped RNA-seq reads to mm10 genes using inbuilt annotation:
-
- featureCounts -a ../annotation/mm10_RefSeq_exon.txt -F 'SAF' -o counts.txt subread_results.bam
-
-Assign mapped RNA-seq reads to hg38 genes using a public GTF annotation:
-
- featureCounts -a hg38_annotation.gtf -o counts.txt subread_results.bam
-
-Tutorials
--------------------
-A short tutorial for Subread - http://bioinf.wehi.edu.au/subread
-A short tutorial for Subjunc - http://bioinf.wehi.edu.au/subjunc
-A short tutorial for featureCounts - http://bioinf.wehi.edu.au/featureCounts
-A short tutorial for exactSNP - http://bioinf.wehi.edu.au/exactSNP
-
-Users Guide
---------------
-Users Guide can be found in the 'doc' subdirectory of this software package or via URL (http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf).
+annotation Directory including NCBI RefSeq gene annotations for multiple versions of human and mouse genomes.
+bin Directory including executables after compilation (or directly available from a binary release).
+doc Directory including the Subread Users Guide.
+LICENSE The license agreement for using this package.
+README.txt This file.
+src Directory including source code (binary releases do not have this directory).
+test Directory including test data and scripts.
Citation
--------------
@@ -89,7 +49,10 @@ If you use the featureCounts program, please cite:
Liao Y, Smyth GK and Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30, 2014
+If you use Subread and featureCounts to map and quantify RNA-seq data, please cite:
+
+Liao Y, Smyth GK and Shi W. The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads. Nucleic Acids Research, 47(8):e47, 2019
+
Mailing lists
--------------
-Please post your questions/suggestions to Bioconductor support site(https://support.bioconductor.org/) or Subread google group (https://groups.google.com/forum/#!forum/subread).
-
+Please post your questions/suggestions to Bioconductor support site (https://support.bioconductor.org/) or Subread google group (https://groups.google.com/forum/#!forum/subread).
=====================================
src/makefile.version
=====================================
@@ -1,4 +1,4 @@
-SUBREAD_VERSION_BASE=2.0.2
+SUBREAD_VERSION_BASE=2.0.3
SUBREAD_VERSION_DATE=$(SUBREAD_VERSION_BASE)-$(shell date +"%d%b%Y")
SUBREAD_VERSION="$(SUBREAD_VERSION_DATE)"
SUBREAD_VERSION="$(SUBREAD_VERSION_BASE)"
=====================================
src/readSummary.c
=====================================
@@ -7733,14 +7733,13 @@ void print_usage()
SUBREADputs("# Parameters specific to paired end reads");
SUBREADputs("");
- SUBREADputs(" -p If specified, libraries are assumed to contain paired-end");
- SUBREADputs(" reads. For any library that contains paired-end reads, the");
- SUBREADputs(" 'countReadPairs' parameter controls if read pairs or reads");
- SUBREADputs(" should be counted.");
+ SUBREADputs(" -p Specify that input data contain paired-end reads. To");
+ SUBREADputs(" perform fragment counting (ie. counting read pairs), the");
+ SUBREADputs(" '--countReadPairs' parameter should also be specified in");
+ SUBREADputs(" addition to this parameter.");
SUBREADputs("");
- SUBREADputs(" --countReadPairs If specified, fragments (or templates) will be counted");
- SUBREADputs(" instead of reads. This option is only applicable for");
- SUBREADputs(" paired-end reads. For single-end data, it is ignored.");
+ SUBREADputs(" --countReadPairs Count read pairs (fragments) instead of reads. This option");
+ SUBREADputs(" is only applicable for paired-end reads.");
SUBREADputs("");
SUBREADputs(" -B Only count read pairs that have both ends aligned.");
SUBREADputs("");
View it on GitLab: https://salsa.debian.org/med-team/subread/-/commit/688c69997ffd190498101d6aaf3ddeb7a3a72ee2
--
View it on GitLab: https://salsa.debian.org/med-team/subread/-/commit/688c69997ffd190498101d6aaf3ddeb7a3a72ee2
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