From 455463d21c8eab6d4fcaa47238b8be523e261d11 Mon Sep 17 00:00:00 2001
From: maxibor <maxime.borry@gmail.com>
Date: Tue, 27 Mar 2018 14:50:36 +0200
Subject: [PATCH] fix in coverage specification

---
 adrsm           |  3 +--
 lib/adrsmlib.py | 18 +++++++-----------
 2 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/adrsm b/adrsm
index d68aeb1..35f2ea8 100755
--- a/adrsm
+++ b/adrsm
@@ -9,7 +9,7 @@ import argparse
 def _get_args():
     '''This function parses and return arguments passed in'''
     parser = argparse.ArgumentParser(
-        prog='ADRSM',
+        prog='ADRSM v0.5',
         description='Ancient DNA Read Simulator for Metagenomics')
     parser.add_argument('confFile', help="path to configuration file")
     parser.add_argument(
@@ -127,7 +127,6 @@ if __name__ == "__main__":
     all_genomes = read_config(INFILE, GENDIR)
     for agenome in all_genomes.keys():
         stat_and_run = ad.run_read_simulation_multi(INFILE=agenome,
-                                                    NREAD=None,
                                                     COV=all_genomes[agenome][1],
                                                     READLEN=READLEN,
                                                     INSERLEN=all_genomes[agenome][0],
diff --git a/lib/adrsmlib.py b/lib/adrsmlib.py
index 315a6c3..8fa3b78 100644
--- a/lib/adrsmlib.py
+++ b/lib/adrsmlib.py
@@ -30,7 +30,7 @@ def scale(x, themin, themax):
 def reverse_complement(dna):
     dna = dna.upper()
     '''
-    Reverse complement a DNA string 
+    Reverse complement a DNA string
     '''
     dna = dna[::-1]
     revcom = []
@@ -159,13 +159,10 @@ def write_fastq_multi(fastq_dict, outputfile):
                     f2.write(reads2)
 
 
-def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1, A2, MINLENGTH, ERR,  DAMAGE, GEOM_P, THEMIN, THEMAX, fastq_dict, QUALITY):
+def run_read_simulation_multi(INFILE, COV, READLEN, INSERLEN, LENDEV, A1, A2, MINLENGTH, ERR,  DAMAGE, GEOM_P, THEMIN, THEMAX, fastq_dict, QUALITY):
     print("===================")
     print("Genome: ", INFILE)
-    if COV:
-        print("Coverage: ", COV)
-    else:
-        print("Number of reads: ", NREAD)
+    print("Coverage: ", COV)
     print("Read length: ", READLEN)
     print("Mean Insert length: ", INSERLEN)
     print("Insert length standard deviation: ", LENDEV)
@@ -178,15 +175,14 @@ def run_read_simulation_multi(INFILE, NREAD, COV, READLEN, INSERLEN, LENDEV, A1,
     basename = get_basename(INFILE)
     fasta = read_fasta(INFILE)
 
-    if COV:
-        nread = int(fasta[1] / INSERLEN)
-        print("Number of reads: ", nread)
-        print("===================\n")
+    nread = int((fasta[1] / INSERLEN) * COV)
+    print("Number of reads: ", nread)
+    print("===================\n")
 
     insert_lengths = [int(n) for n in npr.normal(INSERLEN, LENDEV, nread)]
 
     all_inserts = random_insert(fasta, insert_lengths, READLEN, MINLENGTH)
-    if DAMAGE == True:
+    if DAMAGE:
         all_inserts = add_damage(
             all_inserts=all_inserts,
             geom_p=GEOM_P,