Update run_FREEC_wrapper.pl

Correct a few typos; fixed an issue where max_expected_gc becomes smaller than min_expected_gc
yjx1217 · Apr 12, 2023 · a54562f · a54562f
1 parent 804fdb5
commit a54562f
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/scripts/run_FREEC_wrapper.pl b/scripts/run_FREEC_wrapper.pl
@@ -22,10 +22,10 @@
 #   -read_length_for_mappability 100 \
 #   -window 10000 \
 #   -step 2500 \
-#   -mate_orientation 0 \
+#   -mates_orientation 0 \
 #   -bam input.bam \
 #   -excluded_chr_list excluded_chr_list.txt \
-#   -output_prefix output_prefix
+#   -prefix output_prefix
 ##############################################################
 
 my ($refseq, $bam, $prefix, $ploidy, $threads, $bedtools, $samtools, $gemtools, $gem_mappability, $freec, $window_size, $step_size, $mates_orientation, $read_length_for_mappability, $min_mappability, $min_expected_gc, $max_expected_gc, $excluded_chr_list);
@@ -164,7 +164,7 @@
     if ($gc_quantile_lower_chr > $min_expected_gc) {
 	$min_expected_gc = $gc_quantile_lower_chr;
     }
-    if ($gc_quantile_upper_chr < $max_expected_gc) {
+    if ($gc_quantile_upper_chr < $max_expected_gc && $gc_quantile_upper_chr > $min_expected_gc) {
 	$max_expected_gc = $gc_quantile_upper_chr;
     }
 }
@@ -217,7 +217,7 @@
 print $FREEC_config_fh "[sample]\n";
 print $FREEC_config_fh "inputFormat = BAM\n";
 print $FREEC_config_fh "mateFile = FREEC.bam\n";
-print $FREEC_config_fh "matesOrientation = $mates_orientation\n";
+print $FREEC_config_fh "mateOrientation = $mates_orientation\n";
 close $FREEC_config_fh;
 
 # run FREEC