fixed typos

doc/settings.md

@@ -50,7 +50,7 @@ This section contains general settings:
 * `cnv_bin_size_longread_wgs` - Bin size used for CNV analysis of long-read WGS samples.
 * `use_bwa1` - Flag (true/false) that indicates if BWA mem should be used for mapping instead of BWA mem 2 (BWA mem 2 is faster, but needs more RAM).
 * `annotate_refseq_consequences` - Flag (true/false) that indicates if variant consequences based on RefSeq transcripts should be annotated in addition to variant consequences based on Ensembl transcripts.
-* `custom_colums` - Used to add custom annotations to the output VCF/GSvar file. Each entry consists of a colon-speparated list of VCF file, INFO field name in the source VCF (prefixed with `CUSTOM_` in the annotated VCF) and column description. Provide the annotation using the dictionary syntax of PHP, e.g. `custom_colums['NGSD_counts'] = "/mnt/data/dbs/NGSD/NGSD_germline.vcf.gz;COUNTS;NGSD counts"`.
+* `custom_columns` - Used to add custom annotations to the output VCF/GSvar file. Each entry consists of a colon-speparated list of VCF file, INFO field name in the source VCF (prefixed with `CUSTOM_` in the annotated VCF) and column description. Provide the annotation using the dictionary syntax of PHP, e.g. `custom_columns['NGSD_counts'] = "/mnt/data/dbs/NGSD/NGSD_germline.vcf.gz;COUNTS;NGSD counts"`.
 
 ## Section 'dragen'
 

settings_nightly.ini

@@ -92,8 +92,8 @@ cnv_bin_size_longread_wgs = 10000
 use_bwa1 = false
 file_access_group = f_ad_bi_l_medgen_access_storages
 annotate_refseq_consequences = false
-custom_colums_test['ngsd_counts'] = "/mnt/storage2/users/ahsturm1/megSAP/test/data/an_vep_custom.vcf.gz;COUNTS;NGSD counts"
-custom_colums_test['ngsd_nervous_system'] = "/mnt/storage2/users/ahsturm1/megSAP/test/data/an_vep_custom.vcf.gz;GSC08;NGSD nervous system counts"
+custom_columns_test['ngsd_counts'] = "/mnt/storage2/users/ahsturm1/megSAP/test/data/an_vep_custom.vcf.gz;COUNTS;NGSD counts"
+custom_columns_test['ngsd_nervous_system'] = "/mnt/storage2/users/ahsturm1/megSAP/test/data/an_vep_custom.vcf.gz;GSC08;NGSD nervous system counts"
 
 [dragen]
 ; transfer folder

src/Common/genomics.php

@@ -692,7 +692,7 @@ function load_vcf_normalized($filename)
 		else
 		{
 			$parts = explode("\t", $line);
-			if (count($parts)<10) trigger_error("VCF file $filename has line with less than 10 colums: $line", E_USER_ERROR);
+			if (count($parts)<10) trigger_error("VCF file $filename has line with less than 10 columns: $line", E_USER_ERROR);
 			list($chr, $pos, $id, $ref, $alt, $qual, $filter, $info, $format) = $parts;
 
 

src/NGS/an_vep.php

@@ -127,10 +127,10 @@ function annotation_file_path($rel_path, $is_optional=false)
 //custom annotation using VcfAnnotateFromVcf
 if ($custom!="")
 {
-	$custom_colums = get_path($custom, false);
-	if (is_array($custom_colums))
+	$custom_columns = get_path($custom, false);
+	if (is_array($custom_columns))
 	{
-		foreach($custom_colums as $key => $tmp)
+		foreach($custom_columns as $key => $tmp)
 		{
 			list($vcf, $col, $desc) = explode(";", $tmp, 3);
 			fwrite($config_file, "{$vcf}\tCUSTOM\t{$col}\t\n");

src/NGS/vcf2gsvar.php

@@ -19,11 +19,11 @@
 $parser->addFlag("test", "Run in test mode. Skips replacing sample headers with NGSD information.");
 extract($parser->parse($argv));
 
-$custom_colums = [];
+$custom_columns = [];
 if ($custom!="")
 {
 	$tmp = get_path($custom, false);
-	if (is_array($tmp)) $custom_colums = $tmp;
+	if (is_array($tmp)) $custom_columns = $tmp;
 }
 
 //skip common MODIFIER variants in WGS mode
@@ -359,7 +359,7 @@ function load_hgnc_db()
 );
 
 $column_desc_custom = [];
-foreach($custom_colums as $key => $tmp)
+foreach($custom_columns as $key => $tmp)
 {
 	list($vcf, $col, $desc) = explode(";", $tmp, 3);
 	$column_desc_custom[] = [$key, $desc];
@@ -1530,7 +1530,7 @@ function load_hgnc_db()
 	$cosmic = implode(",", collapse($tag, "COSMIC", $cosmic, "unique"));
 
 	//custom columns
-	foreach($custom_colums as $key => $tmp)
+	foreach($custom_columns as $key => $tmp)
 	{
 		list($vcf, $col, $desc) = explode(";", $tmp, 3);
 		$custom_column_data[$key] = isset($info["CUSTOM_".$col]) ? $info["CUSTOM_".$col] : "";
@@ -1595,7 +1595,7 @@ function load_hgnc_db()
 		fwrite($handle_out, "\t".$in_short_read_sample);
 	}
 
-	foreach($custom_colums as $key => $tmp)
+	foreach($custom_columns as $key => $tmp)
 	{
 		fwrite($handle_out, "\t".$custom_column_data[$key]);
 	}

src/NGS/vcf2gsvar_somatic.php

@@ -25,7 +25,7 @@
 $tmp = $parser->tempFile(".GSvar");
 $args = array("-in $in", "-out $tmp", "-genotype_mode skip");
 if ($updown) $args[] = "-updown";
-$args[] = "-custom custom_colums";
+$args[] = "-custom custom_columns";
 $parser->execTool("NGS/vcf2gsvar.php", implode(" ", $args));
 $gsvar = Matrix::fromTSV($tmp);
 

src/Pipelines/annotate.php

@@ -67,7 +67,7 @@
 if ($somatic) $args[] = "-somatic";
 if ($somatic) $args[] = "-somatic";
 if (get_path("annotate_refseq_consequences", false)) $args[] = "-annotate_refseq_consequences";
-$args[] = "-custom custom_colums";
+$args[] = "-custom custom_columns";
 if ($no_splice) $args[] = "-no_splice";
 $parser->execTool("NGS/an_vep.php", implode(" ", $args));
 
@@ -157,7 +157,7 @@
 	if ($multi) $args[] = "-genotype_mode multi";
 	if ($sys['type']=="WGS") $args[] = "-wgs";
 	if ($sys['type']=="lrGS") $args[] = "-wgs -longread";
-	$args[] = "-custom custom_colums";
+	$args[] = "-custom custom_columns";
 	$parser->execTool("NGS/vcf2gsvar.php", implode(" ", $args));
 
 	//annotate variant allele frequency and depth from related RNA sample, if available

src/Tools/bedpe2somatic.php

@@ -111,7 +111,7 @@ function get_info_fields($comments)
 	return $info_col_description;
 }
 
-//Extracts certain fields from INFO column and returns results as associative array containing the colums.
+//Extracts certain fields from INFO column and returns results as associative array containing the columns.
 //The function returns the keys "flags", "somaticscore" and "junction_somaticscore"
 function expand_info_col($info_col)
 {

test/tool_test_an_vep.php

@@ -36,11 +36,11 @@
 check_file($out_file_dragen, data_folder().$name."_out_dragen.vcf", true);
 
 //DRAGEN and custom annotations
-$custom_colums_test = get_path("custom_colums_test");
-if (is_array($custom_colums_test))
+$custom_columns_test = get_path("custom_columns_test");
+if (is_array($custom_columns_test))
 {
 	$out_file_dragen2 = output_folder().$name."_out_dragen2.vcf";
-	check_exec("php ".src_folder()."/NGS/{$name}.php -test -in ".data_folder().$name."_in_dragen.vcf -out $out_file_dragen2 --log ".output_folder().$name."_out_dragen2.log -custom custom_colums_test");
+	check_exec("php ".src_folder()."/NGS/{$name}.php -test -in ".data_folder().$name."_in_dragen.vcf -out $out_file_dragen2 --log ".output_folder().$name."_out_dragen2.log -custom custom_columns_test");
 	remove_lines_containing($out_file_dragen2, array("##VEP=\"v", "##VEP-command-line='", "##INFO=<ID=NGSD_GENE_INFO,"));
 	check_file($out_file_dragen2, data_folder().$name."_out_dragen2.vcf", true);
 }

test/tool_test_vcf2gsvar.php

@@ -48,11 +48,11 @@
 check_file($out_file_dragen, data_folder().$name."_out_dragen.GSvar", true);
 
 //genotype_mode=single, DRAGEN + custom colunns
-$custom_colums_test = get_path("custom_colums_test");
-if (is_array($custom_colums_test))
+$custom_columns_test = get_path("custom_columns_test");
+if (is_array($custom_columns_test))
 {
 	$out_file_dragen2 = output_folder().$name."_out_dragen2.GSvar";
-	check_exec("php ".src_folder()."/NGS/{$name}.php -in ".data_folder().$name."_in_dragen2.vcf -out $out_file_dragen2 --log ".output_folder().$name."_out_dragen2.log -custom custom_colums_test -test");
+	check_exec("php ".src_folder()."/NGS/{$name}.php -in ".data_folder().$name."_in_dragen2.vcf -out $out_file_dragen2 --log ".output_folder().$name."_out_dragen2.log -custom custom_columns_test -test");
 	remove_lines_containing($out_file_dragen2, "#CREATION_DATE=");
 	check_file($out_file_dragen2, data_folder().$name."_out_dragen2.GSvar", true);
 }