Prep for v1.5.1

README.md

@@ -23,11 +23,11 @@ The documentation for DNMTools can be found
 ## Installation
 
 - **Linux**
-  [binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-Linux.tar.gz).
+  [binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1-Linux.tar.gz).
   Should work on any Linux distribution since roughly 2017.
 
 - **Mac**
-  [binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0-macOS.tar.gz).
+  [binary](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1-macOS.tar.gz).
   Should work on any Mac hardware and macOS-13 (Ventura) or newer.
 
 - **Conda**
@@ -36,7 +36,7 @@ The documentation for DNMTools can be found
   ```
 
 - **Source**
-  [dnmtools-1.5.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0.tar.gz). Dependencies:
+  [dnmtools-1.5.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1.tar.gz). Dependencies:
   [GSL](http://www.gnu.org/software/gsl),
   [HTSlib](https://github.com/samtools/htslib),
   [libdeflate](https://github.com/ebiggers/libdeflate) and
@@ -45,8 +45,8 @@ The documentation for DNMTools can be found
 
   Build DNMTools like this:
   ```console
-  tar -xf dnmtools-1.5.0.tar.gz
-  cd dnmtools-1.5.0
+  tar -xf dnmtools-1.5.1.tar.gz
+  cd dnmtools-1.5.1
   ./configure --prefix=$HOME
   make
   make install

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([dnmtools], [1.5.0], [andrewds@usc.edu],
+AC_INIT([dnmtools], [1.5.1], [andrewds@usc.edu],
         [dnmtools], [https://github.com/smithlabcode/dnmtools])
 dnl the config.h is #included in the sources for version info
 AC_CONFIG_HEADERS([config.h])

data/md5sum.txt

@@ -18,7 +18,7 @@ d41d8cd98f00b204e9800998ecf8427e  tests/two_epialleles.amr
 001b9d966f62fa439b24cf2198cc3de5  tests/reads.counts.sym
 2b8a0406015458be51b8b1c9e58b3602  tests/tRex1_promoters.roi.bed
 9bdb361091d1c0626df30be8ba2c408c  tests/reads.sam
-fa21ade51680ef2752768f02e32eb2e8  tests/reads.xcounts
-14e8f72fde8d0f669b17da6cf4a908b6  tests/reads.unxcounts
-dd6657967ff946ad4f194f1a29051f94  tests/reads.fmt.sam
-5c8375a9f70163f5c89608147fe21693  tests/reads.fmt.srt.uniq.sam
+33640b24cb64ad3179f364af5a887f95  tests/reads.fmt.sam
+b5a63997c57dcde5c3a6635f7beb2cce  tests/reads.fmt.srt.uniq.sam
+3ac2b51545740bafd1a548ba7f73e739  tests/reads.xcounts
+054fe804a32063c80862fbee30f74579  tests/reads.unxcounts

docs/content/abismal.md

@@ -1,8 +1,9 @@
 # abismal - another bisulfite mapping algorithm
 
 ## Synopsis
+
 ```console
-$ dnmtools abismal [OPTIONS] input.fq [input-r2.fq]
+dnmtools abismal [OPTIONS] input.fq [input-r2.fq]
 ```
 
 # Description
@@ -53,10 +54,13 @@ potential mapping locations for reads that begin with their sequence.
 To produce this index run the following command:
 
 ```console
-$ abismalidx  <genome folder or file> <index file>
+$ dnmtools abismalidx genome.fa genome.idx
 ```
 
-For the human genome, whose size is 3 GB, the resulting index is
+Where `genome.fa` is the name of your reference genome, and `genome.idx` is
+what you decided to name your abismal index file (you can name it anything).
+
+For the human genome hg38 reference, with size 3 GB, the resulting index is
 approximately 2.5 GB.
 
 ### Decompressing and isolating paired-end reads
@@ -211,10 +215,10 @@ $ mkdir reads_split
 $ for i in reads/*.txt; do split -a 3 -d -l 12000000 ${i} reads_split/$(basename $i); done
 ```
 
-Notice that the number of lines per split file is 12M, since we want
-3M reads, and there are 4 lines per read. If you split the reads like
-this, you will need to "unsplit" them after the mapping is done. This
-can be done using the `samtools merge` command.
+Notice that the number of lines per split file is 12M, since we want 3M reads,
+and there are 4 lines per read. If you split the reads like this, you will
+need to "unsplit" them after the mapping is done. This can be done using the
+`samtools merge` command.
 
 Abismal also exists as a standalon program, and more details on
 abismal are available in its [documentation

docs/content/format.md

@@ -19,16 +19,20 @@ into a single entry.  SAM/BAM files generated by abismal, Bismark and
 BSMAP can be formatted using the `format` command.
 
 An example use of this command to format a mapped reads file is:
-```shell
-$ dnmtools format -f abismal input.bam output.sam
+
+```console
+dnmtools format -f abismal input.bam output.sam
 ```
+
 Above, the file `input.sam` would have been generated by `abismal`.
 The file `output.bam` is the output, and an output file is required
 here unless the `-stdout` argument is specified (see below). Another
 example:
-```shell
-$ dnmtools format -f abismal -t 8 -B input.bam output.bam
+
+```console
+dnmtools format -f abismal -t 8 -B input.bam output.bam
 ```
+
 This will use 8 threads because of the `-t 8` and will produce output
 in BAM format because of the `-B` flag (not the filename of the
 output).
@@ -94,6 +98,13 @@ unlimited). Normally this parameter is determined during read mapping,
 but `format` can also reject reads that are in opposing strands in the
 same chromosome but map more than this many bases apart.
 
+```txt
+-S, -sam
+```
+The input follows SAM standards for orientation, where reads that map to the
+reverse complement of the reference genome are stored as their reverse
+complement in the SAM/BAM file.
+
 ```txt
 -F, -force
 ```

docs/content/quickstart.md

@@ -70,14 +70,14 @@ would need to be activated when you want to use dnmtools.
 
 ### Configuration
 
-* Download [dnmtools-1.5.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0.tar.gz).
+* Download [dnmtools-1.5.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1.tar.gz).
 * Unpack the archive:
 ```console
-$ tar -zxvf dnmtools-1.5.0.tar.gz
+$ tar -zxvf dnmtools-1.5.1.tar.gz
 ```
 * Move into the dnmtools directory and create a build directory:
 ```console
-$ cd dnmtools-1.5.0
+$ cd dnmtools-1.5.1
 $ mkdir build && cd build
 ```
 * Run the configuration script: