ProphAsm 0.1.2

.clang-format

@@ -0,0 +1,11 @@
+BasedOnStyle: Google
+Language: Cpp
+Standard: Cpp11
+AlignConsecutiveAssignments: true
+SortIncludes: true
+UseTab: Never
+IndentWidth: 4
+IndentCaseLabels: true
+NamespaceIndentation: None
+ColumnLimit: 100
+

CITATION.cff

@@ -0,0 +1,38 @@
+# vim: set ft=yaml ts=2 sts=2 sw=2 expandtab:
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: ProphAsm
+message: >-
+  If you use this software, please cite both the article
+  from preferred-citation and the software itself.
+type: software
+authors:
+  - family-names: Břinda
+    given-names: Karel
+    email: [email protected]
+    orcid: 'https://orcid.org/0000-0003-0200-557X'
+repository-code: 'https://github.com/prophyle/prophasm'
+license: MIT
+doi: 10.5281/zenodo.3887034
+preferred-citation:
+  authors:
+    - family-names: Břinda
+      given-names: Karel
+      email: [email protected]
+      orcid: 'https://orcid.org/0000-0003-0200-557X'
+    - family-names: Baym
+      given-names: Michael
+      email: [email protected]
+      orcid: 'https://orcid.org/0000-0003-1303-5598'
+    - family-names: Kucherov
+      given-names: Gregory
+      email: [email protected]
+      orcid: 'https://orcid.org/0000-0001-5899-5424'
+  type: article
+  title: Simplitigs as an efficient and scalable representation of de Bruijn graphs
+  year: 2021
+  journal: Genome Biology
+  volume: 22
+  doi: 10.1186/s13059-021-02297-z

LICENSE

@@ -1,6 +1,9 @@
 The MIT License
 
-Copyright (c) 2016-2017 Karel Brinda <[email protected]>
+Copyright (c) 2022-     Inria
+              2017-2021 Harvard Medical School
+              2017-2021 Harvard T.H. Chan School of Public Health
+              2015-2016 Universite Paris-Est
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

Makefile

@@ -1,4 +1,4 @@
-.PHONY: all help clean test prophasm readme
+.PHONY: all help clean test prophasm readme format
 
 SHELL=/usr/bin/env bash -eo pipefail
 
@@ -15,6 +15,9 @@ help: ## Print help message
 test:
 	$(MAKE) -C tests
 
+format:
+	clang-format -i src/*.cpp #src/*.h
+
 readme:
 	f=$$(mktemp);\
 	  echo $$f;\

README.md

@@ -8,6 +8,7 @@
 * [Cite](#cite)
 * [Prerequisities](#prerequisities)
 * [Getting started](#getting-started)
+* [How to use](#how-to-use)
 * [Links](#links)
 * [Issues](#issues)
 * [Changelog](#changelog)
@@ -78,38 +79,41 @@ Compute simplitigs:
 ./prophasm -k 15 -i tests/test1.fa -o simplitigs.fa
 ```
 
+
+## How to use
+
 Set operations:
 ```
 ./prophasm -k 15 -i tests/test1.fa -i tests/test2.fa -o _out1.fa -o _out2.fa -x _intersect.fa -s _stats.tsv
    ```
 
 
-## Command line parameters
+## Command-line arguments
 
 <!---
 USAGE-BEGIN
 -->
 ```
-Program:  prophasm (a greedy assembler for k-mer set compression)
-Version:  0.1.1
-Contact:  Karel Brinda <[email protected]>
+Program:  prophasm (computation of simplitigs and k-mer set operations)
+Version:  0.1.2
+Contact:  Karel Brinda <[email protected]>
 
 Usage:    prophasm [options]
 
-Examples: prophasm -k 15 -i f1.fa -i f2.fa -x fx.fa
-             - compute intersection of f1 and f2
-          prophasm -k 15 -i f1.fa -i f2.fa -x fx.fa -o g1.fa -o g2.fa
-             - compute intersection of f1 and f2, and subtract it from them
-          prophasm -k 15 -i f1.fa -o g1.fa
-             - re-assemble f1 to g1
+Examples: prophasm -k 31 -i ref.fa -o simplitigs.fa
+           - compute simplitigs of ref.fa
+          prophasm -k 31 -i ref1.fa -i ref2.fa -x inter.fa
+           - intersect the k-mers sets of ref1 and ref2
+          prophasm -k 31 -i ref1.fa -i ref2.fa -x inter.fa -o dif1.fa -o dif2.fa
+           - intersect ref1 and ref2, and compute the set differences
 
 Command-line parameters:
- -k INT   K-mer size.
- -i FILE  Input FASTA file (can be used multiple times).
- -o FILE  Output FASTA file (if used, must be used as many times as -i).
- -x FILE  Compute intersection, subtract it, save it.
- -s FILE  Output file with k-mer statistics.
- -S       Silent mode.
+ -k INT   k-mer length (from [1, 32])
+ -i FILE  input FASTA file (can be used multiple times)
+ -o FILE  output FASTA file (if used, must be used as many times as -i)
+ -x FILE  compute intersection, subtract it, save it
+ -s FILE  output file with k-mer statistics
+ -S       silent mode
 
 Note that '-' can be used for standard input/output.