Removed the low-quality zones removal.

Hopefully iCLIP data now has better quality and deduplication will be
more efficient taking into account those zones.

CLIP/iCLIP_trim_and_dedup.sh

@@ -67,9 +67,13 @@ count_fastq_reads()
 #             15-17: AT(or GC?)-rich (low diversity)
 #                 [fragment]
 #                        -4 -> -1: 3' UMI
+#strip_low_qual_zones()
+#{
+#    bioawk -c fastx '{print $name"\t"substr($seq, 1, 5)""substr($seq, 12, 3)""substr($seq, 18)"\t"substr($qual, 1, 5)""substr($qual, 12, 3)""substr($qual, 18)}' | mawk '{print "@"$1"\n"$2"\n+\n"$3}'
+#}
 strip_low_qual_zones()
 {
-    bioawk -c fastx '{print $name"\t"substr($seq, 1, 5)""substr($seq, 12, 3)""substr($seq, 18)"\t"substr($qual, 1, 5)""substr($qual, 12, 3)""substr($qual, 18)}' | mawk '{print "@"$1"\n"$2"\n+\n"$3}'
+    bioawk -c fastx '{print "@"$name"\n"$seq"\n+\n"$qual}'
 }
 
 # This script performs 2 sorting and deduplicating operations, depending on the