updated man

doc/rock.pod

@@ -11,7 +11,7 @@
 
 =over 4
 
-=item B<rock> [B<-h>] [B<-i> F<file>] [B<-o> F<file>] [B<-k> F<k_mer_size>]  [B<-q> F<nucl_qual_score_threshold>] [B<-C> F<kappa>] [B<-c> F<kappa_prime>] [B<-l> F<lambda>] [B<-n> F<nb_distinct_k_mer>] [B<-m> F<min_valid_k_mer_per_read>] [Args]
+=item B<rock> [B<-h>] [B<-i> F<file>] [B<-o> F<file>] [B<-k> F<k_mer_size>]  [B<-q> F<nucl_qual_score_threshold>] [B<-C> F<kappa>] [B<-c> F<kappa_prime>] [B<-l> F<lambda>] [B<-n> F<nb_distinct_k_mer>] [B<-m> F<min_valid_k_mer_per_read>] [B<-p>] [Args]
 
 =back
 
@@ -71,6 +71,9 @@ Default is minimum 4.
 Indicate the number of distinct k-mers in input fastq files. 
 This is useful to compute a more appropriate value than the default one for lambda if you have not specified it with -l.
 
+=item -p
+
+Use this flag to process PE separately; ie, a PE is kept if either PE1 or PE2 is below the maximum coverage and removed if either PE1 or PE2 is below the minimum coverage.
 
 =item -v
 
@@ -95,8 +98,7 @@ B<ROCK> is highly parameterizable via its options.
 It is possible to refine filtering by adding more criteria:
     1) nucleotide score threshold: k-mers containing at least 1 nucleotide below specified threshold will not be taken into account.
     2) minimum number of correct k-mers : let X be this number. Reads containing less than X k-mers without nucleotides below threshold will not be processed.
-    They will be put in files named with .undefined extension.
-    3) Pair end reads are processed as single.
+    3) Pair end reads are processed as single or separately.
 
 It is possible to specify the size of the count min sketch by:
     1) indicating the number of arrays that you want in it (via the -l option),