Merge pull request #103 from kbseah/master

Fix bug in using SE reads
HRGV · Feb 11, 2020 · 5b038f4 · 5b038f4
2 parents b448fa0 + ee1f201
commit 5b038f4
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Showing 5 changed files with 21 additions and 11 deletions.
diff --git a/PhyloFlash.pm b/PhyloFlash.pm
@@ -28,7 +28,7 @@ This module contains helper functions shared by the phyloFlash scripts.
 
 =cut
 
-our $VERSION     = "3.3b2";
+our $VERSION     = "3.3b3";
 our @ISA         = qw(Exporter);
 our @EXPORT      = qw(
   $VERSION

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 <img align="right" src="docs/phyloFlash_logo.png" width="200" alt="phyloFlash logo"/>
 
-# phyloFlash v3.3b2
+# phyloFlash v3.3b3
 
 [![GitHub (pre-)release](https://img.shields.io/github/release/HRGV/phyloflash/all.svg?label=Latest%20Version)]()
 [![Bioconda](https://img.shields.io/conda/vn/Bioconda/phyloFlash.svg)](https://bioconda.github.io/recipes/phyloflash/README.html)
@@ -42,11 +42,11 @@ If you clone the repository directly off GitHub you might end up with a version
 
 ```bash
 # Download latest release
-wget https://github.com/HRGV/phyloFlash/archive/pf3.3b2.tar.gz
-tar -xzf pf3.3b2.tar.gz
+wget https://github.com/HRGV/phyloFlash/archive/pf3.3b3.tar.gz
+tar -xzf pf3.3b3.tar.gz
 
 # Check for dependencies and install them if necessary
-cd phyloFlash-pf3.3b2
+cd phyloFlash-pf3.3b3
 ./phyloFlash.pl -check_env
 ```
 

diff --git a/docs/index.md b/docs/index.md
@@ -46,11 +46,11 @@ If you clone the repository directly off GitHub you might end up with a version
 
 ```bash
 # Download latest release
-wget https://github.com/HRGV/phyloFlash/archive/pf3.3b2.tar.gz
-tar -xzf pf3.3b2.tar.gz
+wget https://github.com/HRGV/phyloFlash/archive/pf3.3b3.tar.gz
+tar -xzf pf3.3b3.tar.gz
 
 # Check for dependencies and install them if necessary
-cd phyloFlash-pf3.3b2
+cd phyloFlash-pf3.3b3
 ./phyloFlash.pl -check_env
 ```
 

diff --git a/docs/install.md b/docs/install.md
@@ -52,8 +52,8 @@ If you clone the repository directly off GitHub you might end up with a version
 
 ```bash
 # Download latest release
-wget https://github.com/HRGV/phyloFlash/archive/pf3.3b2.tar.gz
-tar -xzf pf3.3b2.tar.gz
+wget https://github.com/HRGV/phyloFlash/archive/pf3.3b3.tar.gz
+tar -xzf pf3.3b3.tar.gz
 ```
 
 Alternatively clone the latest development version with Git:

diff --git a/phyloFlash.pl b/phyloFlash.pl
@@ -2352,12 +2352,22 @@ sub nhmmer_model_pos {
 
     # Subsample reads with reformat.sh
     my @reformat_args = ("in=$readsf",
-                         "in2=$readsr",
+                         # "in2=$readsr",
                          #"path=$DBHOME",
                          "out=$subsample",
                          "srt=$samplelimit",
                          "ow=t", # Overwrite existing files
                          );
+
+    # Check if SE reads or interleaved reads
+    if ($SEmode == 0) {
+        if ($interleaved == 1) {
+            push @reformat_args, ("interleaved=t");
+        } else {
+            push @reformat_args, ("in2=$readsr");
+        }
+    }
+
     run_prog ("reformat",
               join (" ", @reformat_args),
               undef,