From 9028210eb295348ac5700e79bc29f4e4ccc068fb Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Sun, 10 Aug 2025 20:09:27 -0700 Subject: [PATCH 1/4] Updates to reflect version number bump t v1.5.1 --- README.md | 10 +++++----- configure.ac | 2 +- docs/content/quickstart.md | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index c42d8fdb..3ab81a52 100644 --- a/README.md +++ b/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=$HOME make make install diff --git a/configure.ac b/configure.ac index f314e7f1..ffbc8065 100644 --- a/configure.ac +++ b/configure.ac @@ -14,7 +14,7 @@ dnl but WITHOUT ANY WARRANTY; without even the implied warranty of dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU dnl General Public License for more details. -AC_INIT([dnmtools], [1.5.0], [andrewds@usc.edu], +AC_INIT([dnmtools], [1.5.1], [andrewds@usc.edu], [dnmtools], [https://github.com/smithlabcode/dnmtools]) dnl the config.h is #included in the sources for version info AC_CONFIG_HEADERS([config.h]) diff --git a/docs/content/quickstart.md b/docs/content/quickstart.md index da638db0..1ea54d8d 100644 --- a/docs/content/quickstart.md +++ b/docs/content/quickstart.md @@ -70,14 +70,14 @@ would need to be activated when you want to use dnmtools. ### Configuration -* Download [dnmtools-1.5.0.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.0/dnmtools-1.5.0.tar.gz). +* Download [dnmtools-1.5.1.tar.gz](https://github.com/smithlabcode/dnmtools/releases/download/v1.5.1/dnmtools-1.5.1.tar.gz). * Unpack the archive: ```console -$ 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: From 52e85de5b3613d54fda13fa0f3daeadf5e61e3ab Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Sun, 10 Aug 2025 20:10:02 -0700 Subject: [PATCH 2/4] docs/content/abismal.md: just very minor updates for clarity --- docs/content/abismal.md | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/docs/content/abismal.md b/docs/content/abismal.md index 312da12a..11f3fafb 100644 --- a/docs/content/abismal.md +++ b/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 +$ 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 $i); done ``` -Notice that the number of lines per split file is 12M, since we want -3M reads, and there are 4 lines per read. If you split the reads like -this, you will need to "unsplit" them after the mapping is done. This -can be done using the `samtools merge` command. +Notice that the number of lines per split file is 12M, since we want 3M reads, +and there are 4 lines per read. If you split the reads like this, you will +need to "unsplit" them after the mapping is done. This can be done using the +`samtools merge` command. Abismal also exists as a standalon program, and more details on abismal are available in its [documentation From dd6af68ba9a561fe28c3756106394567913edc6b Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Sun, 10 Aug 2025 20:10:27 -0700 Subject: [PATCH 3/4] docs/content/format.md: adding a description of the argument for when input is strict SAM format --- docs/content/format.md | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/docs/content/format.md b/docs/content/format.md index aafef1fc..5b086a96 100644 --- a/docs/content/format.md +++ b/docs/content/format.md @@ -19,16 +19,20 @@ into a single entry. SAM/BAM files generated by abismal, Bismark and BSMAP can be formatted using the `format` command. An example use of this command to format a mapped reads file is: -```shell -$ 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 ``` From d73acb6a9473748890dfbd4e81cfa8d27f7f3103 Mon Sep 17 00:00:00 2001 From: Andrew D Smith Date: Sun, 10 Aug 2025 20:38:05 -0700 Subject: [PATCH 4/4] data/md5sum.txt: updating hashes for files with version number changes --- data/md5sum.txt | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/data/md5sum.txt b/data/md5sum.txt index 71c0c9ee..738ab53d 100644 --- a/data/md5sum.txt +++ b/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