Updates for new release

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/v3.2.2/abismal-3.2.2.tar.gz
-$ tar -zxvf abismal-3.2.2.tar.gz
-$ cd abismal-3.2.2
+$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+$ tar -zxvf abismal-3.2.4.tar.gz
+$ cd abismal-3.2.4
 $ 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/v3.2.2/abismal-3.2.2.tar.gz
-$ tar -zxvf abismal-3.2.2.tar.gz
-$ cd abismal-3.2.2
+$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+$ tar -zxvf abismal-3.2.4.tar.gz
+$ cd abismal-3.2.4
 ```
 Finally, these steps build the software:
 ```console

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], [3.2.3], [andrewds@usc.edu],
+AC_INIT([abismal], [3.2.4], [andrewds@usc.edu],
         [abismal], [https://github.com/smithlabcode/abismal])
 
 dnl the config.h is not currently #included in the source, and only

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
-299e0bc8d7862326d693a08b9fc70d76  tests/reads_pbat_pe.sam
 ae8e662c3ab23ba742a45a9784390e63  tests/reads_pe_1.fq
 d2723d2e99d2a3492af508633d61b30a  tests/reads_pe_2.fq
 6e2ba01e98f0effc005641ba6a7eb8b6  tests/reads_pe.mstats
-5e661e3bb770f84bee1bf09ff9ec4f30  tests/reads_pe.sam
 2e033e6c0f2e93000877d6f8f40bcc99  tests/reads_rpbat_pe_1.fq
 a28bc47b567130bbcdc45b1daa54ae32  tests/reads_rpbat_pe_2.fq
 ecf7559bdeecb3f5d23e2c85e1eb22ff  tests/reads_rpbat_pe.mstats
-5f1812a2d4e26e6fd447a8bf5fd9b132  tests/reads_rpbat_pe.sam
-b621241624f8a8d030b42dd47838d5dd  tests/reads.sam
 bcbf01be810cbf4051292813eb6b9225  tests/tRex1.idx
+411a91bbd43a429ca665e350ddb96c4b  tests/reads_pbat_pe.sam
+28312ec7f684e8552be4a842e451e9be  tests/reads_rpbat_pe.sam
+7a1dd56c17759819bdc6cca3cf39ef1d  tests/reads.sam
+a067f22b83e6a7cd1246cdc0353b7ce9  tests/reads_pe.sam

docs/MANUAL.md

@@ -49,9 +49,9 @@ substantially.
 
 Run the following commands to install abismal
 ```
-wget https://github.com/smithlabcode/abismal/releases/download/v3.2.2/abismal-3.2.2.tar.gz
-tar -xvzf abismal-3.2.2.tar.gz
-cd abismal-3.2.2
+wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+tar -xvzf abismal-3.2.4.tar.gz
+cd abismal-3.2.4
 ./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:3.2.2  CL:[command-call]
+@PG ID:ABISMAL  VN:3.2.4  CL:[command-call]
 ```
 where [command-call] is the shell command used to run abismal.
 

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/v3.2.2/abismal-3.2.2.tar.gz
-tar -xvzf abismal-3.2.2.tar.gz
-cd abismal-3.2.2
+wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+tar -xvzf abismal-3.2.4.tar.gz
+cd abismal-3.2.4
 \&./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:3.2.2  CL:\[dq][command-call]\[dq]
+\[at]PG ID:ABISMAL  VN:3.2.4  CL:\[dq][command-call]\[dq]
 \f[R]
 .fi
 .PP

docs/abismal.html

@@ -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/v3.2.2/abismal-3.2.2.tar.gz
-tar -xvzf abismal-3.2.2.tar.gz
-cd abismal-3.2.2
+<pre><code>wget https://github.com/smithlabcode/abismal/releases/download/v3.2.4/abismal-3.2.4.tar.gz
+tar -xvzf abismal-3.2.4.tar.gz
+cd abismal-3.2.4
 ./configure --prefix=$(pwd)
 make
 make install</code></pre>
@@ -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:3.2.2  CL:&quot;[command-call]&quot;</code></pre>
+<pre><code>@PG ID:ABISMAL  VN:3.2.4  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>