From 3a121965cc750d0897ffbd89ffba5db57d54cd66 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Sun, 8 Oct 2023 17:19:48 -0700 Subject: [PATCH 1/2] Preparing for v3.2.2 release --- README.md | 12 ++++++------ configure.ac | 2 +- docs/MANUAL.md | 8 ++++---- docs/abismal.1 | 8 ++++---- docs/abismal.html | 8 ++++---- 5 files changed, 19 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 183f010..4efa947 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/v3.2.1/abismal-3.2.1.tar.gz -$ tar -zxvf abismal-3.2.1.tar.gz -$ cd abismal-3.2.1 +$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz +$ tar -zxvf abismal-3.2.2.tar.gz +$ cd abismal-3.2.2 $ 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/v3.2.1/abismal-3.2.1.tar.gz -$ tar -zxvf abismal-3.2.1.tar.gz -$ cd abismal-3.2.1 +$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz +$ tar -zxvf abismal-3.2.2.tar.gz +$ cd abismal-3.2.2 ``` Finally, these steps build the software: ```console diff --git a/configure.ac b/configure.ac index 5f97393..8b97a47 100644 --- a/configure.ac +++ b/configure.ac @@ -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], [3.2.1], [andrewds@usc.edu], +AC_INIT([abismal], [3.2.2], [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 f8612d1..99bba20 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/v3.2.1/abismal-3.2.1.tar.gz -tar -xvzf abismal-3.2.1.tar.gz -cd abismal-3.2.1 +wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz +tar -xvzf abismal-3.2.2.tar.gz +cd abismal-3.2.2 ./configure --prefix=$(pwd) make make install @@ -317,7 +317,7 @@ sequence. The last line of the headers is a copy of how the program was called to generate the SAM output, and is of the form ``` -@PG ID:ABISMAL VN:3.2.1 CL:[command-call] +@PG ID:ABISMAL VN:3.2.2 CL:[command-call] ``` where [command-call] is the shell command used to run abismal. diff --git a/docs/abismal.1 b/docs/abismal.1 index 54ac8f3..0d3e034 100644 --- a/docs/abismal.1 +++ b/docs/abismal.1 @@ -57,9 +57,9 @@ Run the following commands to install abismal .IP .nf \f[C] -wget https://github.com/smithlabcode/abismal/releases/download/v3.2.1/abismal-3.2.1.tar.gz -tar -xvzf abismal-3.2.1.tar.gz -cd abismal-3.2.1 +wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz +tar -xvzf abismal-3.2.2.tar.gz +cd abismal-3.2.2 \&./configure --prefix=$(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:3.2.1 CL:\[dq][command-call]\[dq] +\[at]PG ID:ABISMAL VN:3.2.2 CL:\[dq][command-call]\[dq] \f[R] .fi .PP diff --git a/docs/abismal.html b/docs/abismal.html index 9af86ff..16e2b23 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/v3.2.1/abismal-3.2.1.tar.gz
-tar -xvzf abismal-3.2.1.tar.gz
-cd abismal-3.2.1
+
wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
+tar -xvzf abismal-3.2.2.tar.gz
+cd abismal-3.2.2
 ./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:3.2.1  CL:"[command-call]"

+
@PG ID:ABISMAL  VN:3.2.2  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.


From ef6480f62482b136c602c55cae703f758fbadac0 Mon Sep 17 00:00:00 2001
From: Andrew D Smith 
Date: Sun, 8 Oct 2023 17:26:31 -0700
Subject: [PATCH 2/2] Updating test outputs checksums for v3.2.2

---
 data/md5sum.txt | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/data/md5sum.txt b/data/md5sum.txt
index 9c8b730..afccec1 100644
--- a/data/md5sum.txt
+++ b/data/md5sum.txt
@@ -3,14 +3,14 @@ ddeea92ba05c5c6a909c136d5059140d  tests/reads.mstats
 7c43e9b1409c6725c70aeb18d8db3413  tests/reads_pbat_pe_1.fq
 21c3b088e956de62e10a6d190ffb8744  tests/reads_pbat_pe_2.fq
 8c170b022512012f078396cc19c41600  tests/reads_pbat_pe.mstats
-af67fa9188a9827c9cd880d8fc026c43  tests/reads_pbat_pe.sam
+2882389bdb9fd717076b5ab588a7c1c1  tests/reads_pbat_pe.sam
 ae8e662c3ab23ba742a45a9784390e63  tests/reads_pe_1.fq
 d2723d2e99d2a3492af508633d61b30a  tests/reads_pe_2.fq
 6e2ba01e98f0effc005641ba6a7eb8b6  tests/reads_pe.mstats
-0ae8a7b4afede7409c1ada349c81ad3f  tests/reads_pe.sam
+8f3cb73579f5958b313ed7e4752abd0d  tests/reads_pe.sam
 2e033e6c0f2e93000877d6f8f40bcc99  tests/reads_rpbat_pe_1.fq
 a28bc47b567130bbcdc45b1daa54ae32  tests/reads_rpbat_pe_2.fq
 ecf7559bdeecb3f5d23e2c85e1eb22ff  tests/reads_rpbat_pe.mstats
-39833b8d78aa593c4fd7fe49593aea0c  tests/reads_rpbat_pe.sam
-2c866cec7beba9cdf4b194ce90c0b001  tests/reads.sam
+849e750ec3a7e0220a0eae375cb16b14  tests/reads_rpbat_pe.sam
+b54e2041209f1da8d4402252cbc954c7  tests/reads.sam
 bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx