version 0.3

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "fpa_lr"
-version = "0.2.0"
+version = "0.3.0"
 authors = ["Pierre Marijon <pierre.marijon@inria.fr>"]
 
 description = "fpa filter long read mapping information to save disk space"

Readme.md

@@ -27,6 +27,7 @@ minimap2 long_read.fasta long_read.fasta | fpa -d | gzip - > long_read_dovetail.
 minimap2 long_read.fasta long_read.fasta | fpa -l 500 -L 2000 > match_between_500_2000.paf
 minimap2 long_read.fasta long_read.fasta | fpa -s -m read_1 > no_self_match_no_read_1.paf
 minimap2 long_read.fasta long_read.fasta | fpa -s -r rename.csv > no_self_match_renamed_read_1.paf
+minimap2 long_read.fasta long_read.fasta | fpa -s -r rename.csv -g gfa1 > no_self_match_renamed_read_1.gfa
 ```
 
 ### Rename option
@@ -43,6 +44,14 @@ If the name of the read does not exist in the file it will not be replaced.
 
 If the path passed as parameter does not exist, the names will automatically be replaced by a number, a file like above example will be created.
 
+### Output mode
+
+You can get an output in gfa format with the -o option (--output-mode), two modes are available:
+- basic: the output and in the format that the input
+- gfa1: the output is in gfa1 format
+
+In gfa1 mode options -C and -I indicate that containments and internalmatches are included in the gfa (default option enabled), -c and -i indicate that containments and internalmatches should not be included.
+
 ## Rationale
 
 Long Read mapping tools provides all match they found in read dataset, for many usage some of match aren't usfull, this programme provide some filter to remove it. 
@@ -80,7 +89,7 @@ conda install fpa
 ```
 git clone https://github.com/natir/fpa.git
 cd fpa
-git checkout v0.2
+git checkout v0.3
 
 cargo build
 cargo test

src/cli.rs

@@ -34,32 +34,32 @@ use clap::{App, Arg, ArgMatches};
 
 pub fn parser<'a>() -> ArgMatches<'a> {
     App::new("fpa")
-        .version("0.2 Beedrill")
+        .version("0.3 Meowth")
         .author("Pierre Marijon <pierre.marijon@inria.fr>")
         .about("fpa take long read mapping information and filter them")
         .arg(Arg::with_name("delete_containment")
              .short("c")
              .display_order(10)
              .long("delete-containment")
-             .help("If match are containment match is discard")
+             .help("If match are containment match is discard, in gfa1 mode containment is not included")
              )
         .arg(Arg::with_name("keep_containment")
              .short("C")
              .display_order(20)
              .long("keep-containment")
-             .help("Only containment match is keeped")
+             .help("Only containment match is keeped, in gfa1 mode containment is included")
              )
         .arg(Arg::with_name("delete_internalmatch")
              .short("i")
              .display_order(30)
              .long("delete-internalmatch")
-             .help("If match are an internal match is discard")
+             .help("If match are an internal match is discard, in gfa1 mode internalmatch is not included")
              )
         .arg(Arg::with_name("keep_internalmatch")
              .short("I")
              .display_order(40)
              .long("keep-internalmatch")
-             .help("Only internal match overlap is keeped")
+             .help("Only internal match overlap is keeped, in gfa1 mode internalmatch is included")
              )
         .arg(Arg::with_name("delete_dovetail")
              .short("d")
@@ -144,7 +144,7 @@ pub fn parser<'a>() -> ArgMatches<'a> {
              .possible_values(&["paf", "mhap"])
              )
         .arg(Arg::with_name("mode")
-             .short("g")
+             .short("o")
              .long("output-mode")
              .display_order(120)
              .takes_value(true)