Added --no-mei flag to skip MEI clustering

Makefile

@@ -1,5 +1,5 @@
 TARDIS_VERSION := "1.0.6"
-TARDIS_UPDATE := "September 26, 2019"
+TARDIS_UPDATE := "December 04, 2019"
 TARDIS_DEBUG := 0
 BUILD_DATE := "$(shell date)"
 CC=gcc

bamonly.c

@@ -653,7 +653,7 @@ void bamonly_vh_clustering( bam_info** in_bams, parameters *params)
 				continue;
 			}
 			else
-			        any_in_bam = 1;
+				any_in_bam = 1;
 
 			in_bams[bam_index]->iter = sam_itr_queryi( in_bams[bam_index]->bam_file_index, chr_index_bam, 0, params->this_sonic->chromosome_lengths[chr_index]);
 			if( in_bams[bam_index]->iter == NULL)
@@ -787,16 +787,19 @@ void bamonly_vh_clustering( bam_info** in_bams, parameters *params)
 		fflush( stderr);
 
 		/* Mei */
-		fprintf( stderr, "\nPreparing MEI clusters");
-		initializeReadMapping_MEI( in_bams, params, chr_index);
-		fprintf( stderr, "..");
-		fflush( stderr);
-		MEICluster_Region( params, chr_index);
-		fprintf( stderr, "..");
-		fflush( stderr);
-		vh_finalizeReadMapping_Mei( params->this_sonic->chromosome_lengths[chr_index]);
-		fprintf( stderr, "..");
-		fflush( stderr);
+		if( params->no_interdup == 0)
+		{
+			fprintf( stderr, "\nPreparing MEI clusters");
+			initializeReadMapping_MEI( in_bams, params, chr_index);
+			fprintf( stderr, "..");
+			fflush( stderr);
+			MEICluster_Region( params, chr_index);
+			fprintf( stderr, "..");
+			fflush( stderr);
+			vh_finalizeReadMapping_Mei( params->this_sonic->chromosome_lengths[chr_index]);
+			fprintf( stderr, "..");
+			fflush( stderr);
+		}
 
 		/* NumT */
 		if( ( strcmp( params->this_sonic->chromosome_names[chr_index], "MT") != 0)
@@ -870,18 +873,18 @@ void bamonly_vh_clustering( bam_info** in_bams, parameters *params)
 		free_the_rest( in_bams, params);
 	}
 
-	
+
 	fprintf( stderr, "\n");
 	fclose( fpVcf);
 
 	if ( !any_in_bam)
-	  {
-	    fprintf( stderr, "No chromosome is found in the input BAM/CRAM. Your SONIC and/or reference FASTA files do not match the reference used to generate the alignment file(s).\n");
-	    fprintf( stderr, "Check the reference genome versions and make sure you use the correct SONIC and reference FASTA files.\n");
-	    exit(EXIT_WRONG_SONIC);
-	  }
+	{
+		fprintf( stderr, "No chromosome is found in the input BAM/CRAM. Your SONIC and/or reference FASTA files do not match the reference used to generate the alignment file(s).\n");
+		fprintf( stderr, "Check the reference genome versions and make sure you use the correct SONIC and reference FASTA files.\n");
+		exit(EXIT_WRONG_SONIC);
+	}
+
 
-
 	if( debug_mode)
 		fclose( fileOutput);
 

cmdline.c

@@ -32,7 +32,7 @@ int parse_command_line( int argc, char** argv, parameters* params)
 {
 	int index;
 	int o;
-	static int sensitive = 0, no_soft_clip = 0, debug = 0, no_interdup = 0;
+	static int sensitive = 0, no_soft_clip = 0, debug = 0, no_interdup = 0, no_mei = 0;
 	static int skip_mrfast = 0, quick = 0, ten_x = 0, output_hs = 0, alt_mapping = 0, resolved = 0;
 	static int make_sonic = 0;
 	static int load_sonic = 0;
@@ -68,6 +68,7 @@ int parse_command_line( int argc, char** argv, parameters* params)
 			{"read-cluster", required_argument, 0, 'k'},
 			{"no-soft-clip", no_argument, &no_soft_clip, 1 },
 			{"no-interdup", no_argument, &no_interdup, 1 },
+			{"no-mei", no_argument, &no_mei, 1 },
 			{"debug", no_argument, &debug, 1 },
 			{"xa", no_argument, &alt_mapping, 1 },
 			{"resolved", no_argument, &resolved, 1 },
@@ -333,6 +334,7 @@ int parse_command_line( int argc, char** argv, parameters* params)
 	params->number_of_different_mei_types = count_mei_columns( params->mei);
 	params->alt_mapping = alt_mapping;
 	params->no_interdup = no_interdup;
+	params->no_mei = no_mei;
 	params->seq_resolved = resolved;
 
 	debug_mode = debug;
@@ -382,8 +384,9 @@ void print_help( void)
 	fprintf( stdout, "\t--mei   [\"Alu:L1:SVA\"]     : List of mobile element names.\n");
 	fprintf( stdout, "\t--no-soft-clip             : Skip soft clip remapping.\n");
 	fprintf( stdout, "\t--no-interdup              : Skip interspersed duplication clustering.\n");
+	fprintf( stdout, "\t--no-mei              	   : Skip mobile element insertion (MEI) clustering.\n");
 	fprintf( stdout, "\t--resolved                 : Output sequence resolved vcf calls.\n");
-	fprintf( stdout, "\t--xa                       : Look for the alternative mapping locations in BWA.\n");
+	//fprintf( stdout, "\t--xa                       : Look for the alternative mapping locations in BWA.\n");
 	fprintf( stdout, "\t--first-chr [chr_index]	   : Start running from a specific chromosome [0-based index in reference file].\n");
 	fprintf( stdout, "\t--last-chr [chr_index]	   : Run up to a specific chromosome [0-based index in reference file].\n");
 

common.h

@@ -111,6 +111,7 @@ typedef struct _params
 	int alt_mapping; /* check the alternative mapping locations from the xa field in bwa */
 	int seq_resolved; /* whether to output sequence resolved calls */
 	int no_interdup; /* whether to cluster interspersed duplications */
+	int no_mei; /* whether to cluster mobile element insertions */
 	char skip_mrfast; /* boolean stand-in to skip mrFast mapping (If you already have the divet file created) */
 	int threads; /* number of threads to use for parallel mrFAST, and maybe future parallelization of TARDIS */
 	int num_bams; /* number of input BAM files */