From 136fef20007ba5f33c119ce0456fd7b7b9a19e9f Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Fri, 4 Aug 2023 19:44:40 -0700 Subject: [PATCH] Updating version numbers to 3.2.0 --- README.md | 12 ++++++------ configure.ac | 4 ++-- docs/MANUAL.md | 8 ++++---- docs/abismal.1 | 8 ++++---- docs/abismal.html | 8 ++++---- 5 files changed, 20 insertions(+), 20 deletions(-) diff --git a/README.md b/README.md index 2c976f3..20e04e2 100644 --- a/README.md +++ b/README.md @@ -53,9 +53,9 @@ If you don't have adminstrator privileges, there are other options. If you have the `libhts-dev` installed, to build `abismal` the following should work: ```console -$ wget https://github.com/smithlabcode/abismal/releases/download/v3.1.1/abismal-3.1.1.tar.gz -$ tar -zxvf abismal-3.1.1.tar.gz -$ cd abismal-3.1.1 +$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz +$ tar -zxvf abismal-3.2.0.tar.gz +$ cd abismal-3.2.0 $ mkdir build && cd build $ ../configure --prefix=/where/you/want/abismal $ make @@ -84,9 +84,9 @@ be needed below. If you don't already have `abismal` downloaded, the next step is to download it. Here we will assume you are using a release rather than a clone. To build from a clone involves at least one more step. ```console -$ wget https://github.com/smithlabcode/abismal/releases/download/v3.1.1/abismal-3.1.1.tar.gz -$ tar -zxvf abismal-3.1.1.tar.gz -$ cd abismal-3.1.1 +$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz +$ tar -zxvf abismal-3.2.0.tar.gz +$ cd abismal-3.2.0 ``` Finally, these steps build the software: ```console diff --git a/configure.ac b/configure.ac index d2d00bf..1e65948 100644 --- a/configure.ac +++ b/configure.ac @@ -1,6 +1,6 @@ dnl This file is part of abismal dnl -dnl Copyright (C) 2019-2022: Andrew D. Smith and Guilherme de Sena Brandine +dnl Copyright (C) 2019-2023: Andrew D. Smith and Guilherme de Sena Brandine dnl dnl Authors: Andrew D. Smith and Guilherme de Sena Brandine dnl @@ -14,7 +14,7 @@ dnl but WITHOUT ANY WARRANTY; without even the implied warranty of dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU dnl General Public License for more details. -AC_INIT([abismal], [3.1.1], [andrewds@usc.edu], +AC_INIT([abismal], [3.2.0], [andrewds@usc.edu], [abismal], [https://github.com/smithlabcode/abismal]) dnl the config.h is not currently #included in the source, and only diff --git a/docs/MANUAL.md b/docs/MANUAL.md index 4ef602f..b5e8356 100644 --- a/docs/MANUAL.md +++ b/docs/MANUAL.md @@ -49,9 +49,9 @@ substantially. Run the following commands to install abismal ``` -wget https://github.com/smithlabcode/abismal/releases/download/v3.1.1/abismal-3.1.1.tar.gz -tar -xvzf abismal-3.1.1.tar.gz -cd abismal-3.1.1 +wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz +tar -xvzf abismal-3.2.0.tar.gz +cd abismal-3.2.0 ./configure --prefix=$(pwd) make make install @@ -317,7 +317,7 @@ sequence. The last line of the headers is a copy of how the program was called to generate the SAM output, and is of the form ``` -@PG ID:ABISMAL VN:3.1.1 CL:"[command-call]" +@PG ID:ABISMAL VN:3.2.0 CL:[command-call] ``` where [command-call] is the shell command used to run abismal. diff --git a/docs/abismal.1 b/docs/abismal.1 index 01c97a8..448698d 100644 --- a/docs/abismal.1 +++ b/docs/abismal.1 @@ -57,9 +57,9 @@ Run the following commands to install abismal .IP .nf \f[C] -wget https://github.com/smithlabcode/abismal/releases/download/v3.1.1/abismal-3.1.1.tar.gz -tar -xvzf abismal-3.1.1.tar.gz -cd abismal-3.1.1 +wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz +tar -xvzf abismal-3.2.0.tar.gz +cd abismal-3.2.0 \&./configure --prefix=$(pwd) make make install @@ -364,7 +364,7 @@ generate the SAM output, and is of the form .IP .nf \f[C] -\[at]PG ID:ABISMAL VN:3.1.1 CL:\[dq][command-call]\[dq] +\[at]PG ID:ABISMAL VN:3.2.0 CL:\[dq][command-call]\[dq] \f[R] .fi .PP diff --git a/docs/abismal.html b/docs/abismal.html index 48fa4c5..cd8f0b7 100644 --- a/docs/abismal.html +++ b/docs/abismal.html @@ -65,9 +65,9 @@

DESCRIPTION

absimal was built to map short reads of up to 250 bases. It should successfully map reads of size up to 1 million, but because it uses very short seeds for filtration, the mapping time will increase substantially.

QUICK INSTALLATION

Run the following commands to install abismal

-
wget https://github.com/smithlabcode/abismal/releases/download/v3.1.1/abismal-3.1.1.tar.gz
-tar -xvzf abismal-3.1.1.tar.gz
-cd abismal-3.1.1
+
wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz
+tar -xvzf abismal-3.2.0.tar.gz
+cd abismal-3.2.0
 ./configure --prefix=$(pwd)
 make
 make install

@@ -204,7 +204,7 @@ 
Output headers

 
@SQ SN:[chrom-name] LN:[chrom-length]

 
where [chrom-name] is given by the first word of the chromosome name in the FASTA file (anything after the first white space is deleted), and [chrom-length] is the number of bases in the chromosome sequence.

 
The last line of the headers is a copy of how the program was called to generate the SAM output, and is of the form

-
@PG ID:ABISMAL  VN:3.1.1  CL:"[command-call]"

+
@PG ID:ABISMAL  VN:3.2.0  CL:"[command-call]"

 
where [command-call] is the shell command used to run abismal.

 
Output mapped lines

 
Following the header lines, reads that are mapped once (or at least once if the -a flag is used) are reported. Each read is a set of thirteen tab-separated fields as follows.