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andrewdavidsmith merged 2 commits into from
Oct 9, 2023
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Preparing for v3.2.2 release #43

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3a12196
Preparing for v3.2.2 release
andrewdavidsmith Oct 9, 2023
ef6480f
Updating test outputs checksums for v3.2.2
andrewdavidsmith Oct 9, 2023
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion configure.ac
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Expand Up @@ -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
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8 changes: 4 additions & 4 deletions data/md5sum.txt
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Expand Up @@ -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
8 changes: 4 additions & 4 deletions docs/MANUAL.md
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Expand Up @@ -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
Expand Down Expand Up @@ -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.

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8 changes: 4 additions & 4 deletions docs/abismal.1
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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8 changes: 4 additions & 4 deletions docs/abismal.html
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Expand Up @@ -65,9 +65,9 @@ <h1 id="description">DESCRIPTION</h1>
<p>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.</p>
<h1 id="quick-installation">QUICK INSTALLATION</h1>
<p>Run the following commands to install abismal</p>
<pre><code>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
<pre><code>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</code></pre>
Expand Down Expand Up @@ -204,7 +204,7 @@ <h2 id="output-headers">Output headers</h2>
<pre><code>@SQ SN:[chrom-name] LN:[chrom-length]</code></pre>
<p>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.</p>
<p>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</p>
<pre><code>@PG ID:ABISMAL VN:3.2.1 CL:&quot;[command-call]&quot;</code></pre>
<pre><code>@PG ID:ABISMAL VN:3.2.2 CL:&quot;[command-call]&quot;</code></pre>
<p>where [command-call] is the shell command used to run abismal.</p>
<h2 id="output-mapped-lines">Output mapped lines</h2>
<p>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.</p>
Expand Down