Merge pull request #32 from smithlabcode/version-3.2.0

Version 3.2.0

Author: andrewdavidsmith

Makefile.am

@@ -1,8 +1,8 @@
 # This file is part of abismal
 #
-# Copyright (C) 2018-2020: Andrew D. Smith
+# Copyright (C) 2018-2023: Andrew D. Smith and Guilherme de Sena Brandine
 #
-# Authors: Andrew D. Smith
+# Authors: Andrew D. Smith and Guilherme de Sena Brandine
 #
 # This is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by

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/v3.1.1/abismal-3.1.1.tar.gz
-$ tar -zxvf abismal-3.1.1.tar.gz
-$ cd abismal-3.1.1
+$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz
+$ tar -zxvf abismal-3.2.0.tar.gz
+$ cd abismal-3.2.0
 $ 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/v3.1.1/abismal-3.1.1.tar.gz
-$ tar -zxvf abismal-3.1.1.tar.gz
-$ cd abismal-3.1.1
+$ wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz
+$ tar -zxvf abismal-3.2.0.tar.gz
+$ cd abismal-3.2.0
 ```
 Finally, these steps build the software:
 ```console

configure.ac

@@ -1,6 +1,6 @@
 dnl This file is part of abismal
 dnl
-dnl Copyright (C) 2019-2022: Andrew D. Smith and Guilherme de Sena Brandine
+dnl Copyright (C) 2019-2023: Andrew D. Smith and Guilherme de Sena Brandine
 dnl
 dnl Authors: Andrew D. Smith and Guilherme de Sena Brandine
 dnl
@@ -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], [3.1.1], [andrewds@usc.edu],
+AC_INIT([abismal], [3.2.0], [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

@@ -4,15 +4,14 @@
 b9699416969133224b620f05af97ac90  tests/reads_pbat_pe_1.fq
 12c9d36ab3bf2b9ecb5683d7a093a10d  tests/reads_pbat_pe_2.fq
 3edbf931e6f0da55a50b24e01a975565  tests/reads_pbat_pe.mstats
-51b695cd3aeb3cead392821628acf0f1  tests/reads_pbat_pe.sam
-58d6c1157b187a66d43087fe3e70a38c  tests/reads_pbat.sam
 8e5ad0faefe241de9c2c5748e005e2e8  tests/reads_pe_1.fq
 4ebacfec717182fafce46b037591b228  tests/reads_pe_2.fq
 072a7df62d45dc3d3d4350d79efc9ca1  tests/reads_pe.mstats
-56318794f9e55549c9050a636161e883  tests/reads_pe.sam
 e66339e591563032af436ca2af9b75b1  tests/reads_rpbat_pe_1.fq
 aed5705c4a99601d5799fc8ee42af5b2  tests/reads_rpbat_pe_2.fq
 da00a63969113e09406b61cbe280daa5  tests/reads_rpbat_pe.mstats
-7f3f547ff06296ef2fcc7d1cb8169766  tests/reads_rpbat_pe.sam
-50ec2af709639fa242654f9b3a46981b  tests/reads.sam
 3ba5a1c4c420ca7a2dbd88290033c3bc  tests/tRex1.idx
+cd4a9d6b8c9b00254c53e3e5e5cd249e  tests/reads_pbat_pe.sam
+c466e11e3ed0bfe32c4baa1f16096a95  tests/reads_pe.sam
+c5bf84d3e4e01e27804d39321569c11c  tests/reads_rpbat_pe.sam
+9cab40d2130b4eb9d95f5694d184a5e1  tests/reads.sam

docs/MANUAL.md

@@ -49,9 +49,9 @@ substantially.
 
 Run the following commands to install abismal
 ```
-wget https://github.com/smithlabcode/abismal/releases/download/v3.1.1/abismal-3.1.1.tar.gz
-tar -xvzf abismal-3.1.1.tar.gz
-cd abismal-3.1.1
+wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz
+tar -xvzf abismal-3.2.0.tar.gz
+cd abismal-3.2.0
 ./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:3.1.1  CL:"[command-call]"
+@PG ID:ABISMAL  VN:3.2.0  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/v3.1.1/abismal-3.1.1.tar.gz
-tar -xvzf abismal-3.1.1.tar.gz
-cd abismal-3.1.1
+wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz
+tar -xvzf abismal-3.2.0.tar.gz
+cd abismal-3.2.0
 \&./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:3.1.1  CL:\[dq][command-call]\[dq]
+\[at]PG ID:ABISMAL  VN:3.2.0  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/v3.1.1/abismal-3.1.1.tar.gz
-tar -xvzf abismal-3.1.1.tar.gz
-cd abismal-3.1.1
+<pre><code>wget https://github.com/smithlabcode/abismal/releases/download/v3.2.0/abismal-3.2.0.tar.gz
+tar -xvzf abismal-3.2.0.tar.gz
+cd abismal-3.2.0
 ./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:3.1.1  CL:&quot;[command-call]&quot;</code></pre>
+<pre><code>@PG ID:ABISMAL  VN:3.2.0  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>

src/abismal.cpp

@@ -18,6 +18,7 @@
 #include "abismal.hpp"
 
 #include <bamxx.hpp>
+#include <config.h>
 #include <htslib/bgzf.h>
 #include <htslib/hfile.h>
 #include <htslib/sam.h>
@@ -171,9 +172,9 @@ update_max_read_length(size_t &max_length, const vector<string> &reads) {
 }
 
 struct se_element {  // size = 8
-  score_t diffs;  // 2 bytes
-  flags_t flags;  // 2 bytes
-  uint32_t pos;   // 4 bytes
+  score_t diffs;     // 2 bytes
+  flags_t flags;     // 2 bytes
+  uint32_t pos;      // 4 bytes
 
   se_element(): diffs(MAX_DIFFS), flags(0), pos(0) {}
 
@@ -2041,8 +2042,7 @@ file_exists(const string &filename) {
 }
 
 static int
-abismal_make_sam_header(const ChromLookup &cl, const string program_name,
-                        const string program_version, const int argc,
+abismal_make_sam_header(const ChromLookup &cl, const int argc,
                         const char **argv, bamxx::bam_header &hdr) {
   assert(cl.names.size() > 2);  // two entries exist for the padding
   assert(cl.starts.size() == cl.names.size() + 1);
@@ -2060,14 +2060,13 @@ abismal_make_sam_header(const ChromLookup &cl, const string program_name,
 
   // chromosome sizes
   const size_t n_chroms = names.size();
-  for (size_t i = 0; i < n_chroms; ++i) {
+  for (size_t i = 0; i < n_chroms; ++i)
     out << "@SQ" << '\t' << "SN:" << names[i] << '\t' << "LN:" << sizes[i]
         << '\n';
-  }
 
   // program details
-  out << "@PG" << '\t' << "ID:" << program_name << '\t'
-      << "VN:" << program_version << '\t';
+  out << "@PG" << '\t' << "ID:"
+      << "ABISMAL" << '\t' << "VN:" << VERSION << '\t';
 
   // how the program was run
   std::ostringstream the_command;
@@ -2082,7 +2081,6 @@ abismal_make_sam_header(const ChromLookup &cl, const string program_name,
 int
 abismal(int argc, const char **argv) {
   try {
-    static const string ABISMAL_VERSION = "3.1.1";
     bool VERBOSE = false;
     bool GA_conversion = false;
     bool allow_ambig = false;
@@ -2248,8 +2246,7 @@ abismal(int argc, const char **argv) {
     if (!out) throw runtime_error("failed to open output file: " + outfile);
 
     bamxx::bam_header hdr;
-    int ret = abismal_make_sam_header(abismal_index.cl, "ABISMAL",
-                                      ABISMAL_VERSION, argc, argv, hdr);
+    int ret = abismal_make_sam_header(abismal_index.cl, argc, argv, hdr);
 
     if (ret < 0) throw runtime_error("error formatting header");