diff --git a/processbam.c b/processbam.c
index 4fd2e0e..f251eaa 100644
--- a/processbam.c
+++ b/processbam.c
@@ -28,8 +28,9 @@ void load_bam( parameters *params, configuration *cfg, bam_info* in_bam, char* p
 	int* fragment_size_total;
 	float* variance;
 	char* library_name = NULL;
-	int i, j, library_index, diff, return_value;
+	int i, j, k, library_index, diff, return_value, temp;
 	char fai_file[MAX_SEQ];
+	double count;
 
 	fprintf( stderr, "Processing BAM file %s.\n", path);
 
@@ -100,10 +101,10 @@ void load_bam( parameters *params, configuration *cfg, bam_info* in_bam, char* p
 	/* For SAMPLEFRAG number of alignments, store the template length field.
 	 Performed for each different library */
 	fragment_size = ( int**) getMem( in_bam->num_libraries * sizeof( int*));
-	
+
 	for( i = 0; i < in_bam->num_libraries; i++)
 	{
-	        fragment_size[i] = NULL;
+		fragment_size[i] = NULL;
 		fragment_size[i] = ( int*) getMem( SAMPLEFRAG * sizeof( int));
 	}
 
@@ -163,8 +164,23 @@ void load_bam( parameters *params, configuration *cfg, bam_info* in_bam, char* p
 		/* Sort the fragment sizes */
 		qsort( fragment_size[i], SAMPLEFRAG, sizeof( int), compare_size_int);
 
+		/* When the library does not have sufficient number of reads, we discard the leading 0s when calculating the median */
+		count = 0;
+		if( fragments_sampled[i] < SAMPLEFRAG)
+		{
+			for( k = 0; k < SAMPLEFRAG; k++)
+			{
+				if( fragment_size[i][k] == 0)
+					count++;
+				else
+					break;
+			}
+		}
 		/* Get the medians */
-		( in_bam->libraries)[i]->frag_med = fragment_size[i][( SAMPLEFRAG / 2) - 1];
+		temp = ( fragments_sampled[i] / 2) - 1 + (int) count;
+		( in_bam->libraries)[i]->frag_med = fragment_size[i][temp];
+
+		//fprintf(stderr,"There are %d 0s, %d fragments, index %d and median is %d\n", (int) count, fragments_sampled[i], temp, ( in_bam->libraries)[i]->frag_med);
 	}
 
 	/* Find the fragment sizes which pass the second test, and will contribute to the avg and std */
@@ -195,7 +211,6 @@ void load_bam( parameters *params, configuration *cfg, bam_info* in_bam, char* p
 				second_test_pass[i] = second_test_pass[i] + 1;
 			}
 		}
-
 	}
 
 	for( i = 0; i < in_bam->num_libraries; i++)
@@ -404,6 +419,15 @@ void create_fastq( bam_info* in_bam, char* bam_path, parameters* params)
 	}
 }
 
+void is_library_valid( struct library_properties* in_lib)
+{
+	if( in_lib->frag_avg >=0 && in_lib->frag_std >=0 && in_lib->read_length >= 0 && in_lib->conc_min>=0 && in_lib->conc_max >=0)
+		in_lib->is_valid = true;
+	else
+		in_lib->is_valid = false;
+}
+
+
 void set_library_min_max( struct library_properties* in_lib)
 {
 	in_lib->conc_min = in_lib->frag_avg - ( 4 * in_lib->frag_std);
diff --git a/processfq.h b/processfq.h
index 00b99ad..e1a7f9c 100644
--- a/processfq.h
+++ b/processfq.h
@@ -36,6 +36,7 @@ typedef struct library_properties
 	char *divet; /* file name for the DIVET file post mrfast mapping */
 	int read_length; /* length of reads for this library */
 	int num_sequences; /* number of paired-end sequences for this library */
+	bool is_valid; /* Checks if the library is valid, i.e., mean, conc_min, conc_max, etc. */
 
 	struct softClip *listSoftClip;
 	struct discordantMapping **mappings_discordant;
diff --git a/variants.c b/variants.c
index 3677bb1..b55424d 100644
--- a/variants.c
+++ b/variants.c
@@ -183,7 +183,7 @@ void print_strvar( bam_info** in_bams, parameters* params, struct strvar* sv, FI
 		/* Find ref and alt sequences */
 		seq = readRefAltSeq( params, sv->chr_name, sv->inner_start, sv->inner_end);
 
-		if( params->seq_resolved != 0 && seq != NULL)
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
 			fprintf( fpOut, "%s\t%i\t%s%d\t%s\t%c\t255\t%s\t", sv->chr_name, ( sv->inner_start) + 1, "vh_del_", ++del_cnt, seq, seq[0], ( sv->filtered == false) ? "PASS" : "LowQual");
 		}
@@ -232,7 +232,7 @@ void print_strvar( bam_info** in_bams, parameters* params, struct strvar* sv, FI
 	{
 		seq = readRefAltSeq( params, sv->chr_name, sv->outer_start, sv->outer_end);
 
-		if( params->seq_resolved != 0 && seq != NULL)
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
 			/* Find ref and alt sequences */
 			seq_rev = reverseComplement( seq);
@@ -256,11 +256,11 @@ void print_strvar( bam_info** in_bams, parameters* params, struct strvar* sv, FI
 	else if( sv->svtype == MEIFORWARD)
 	{
 		seq = readRefAltSeqMEI( params, sv->chr_name, sv->mei_name);
-		if(seq != NULL)
-			sv_len = strlen(seq);
 
+		if( seq != NULL)
+			sv_len = strlen(seq);
 
-		if( params->seq_resolved != 0)
+		if( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE)
 		{
 			if( seq != NULL)
 				fprintf( fpOut, "%s\t%i\t%s%d\t%c\t%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1, "vh_mei_", ++mei_cnt, seq[0], seq, 255, ( sv->filtered == false) ? "PASS" : "mfilt");
@@ -287,7 +287,7 @@ void print_strvar( bam_info** in_bams, parameters* params, struct strvar* sv, FI
 		if(seq != NULL)
 			sv_len = strlen(seq);
 
-		if( params->seq_resolved != 0)
+		if( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE)
 		{
 			if( seq != NULL)
 			{
@@ -332,7 +332,7 @@ void print_strvar( bam_info** in_bams, parameters* params, struct strvar* sv, FI
 	{
 		seq = readRefAltSeq( params, sv->chr_name, sv->outer_start, sv->outer_end);
 
-		if( params->seq_resolved != 0 && seq != NULL)
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
 			fprintf( fpOut, "%s\t%i\t%s%d\t%c\t%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, seq[0], seq, 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		}
@@ -350,52 +350,92 @@ void print_strvar( bam_info** in_bams, parameters* params, struct strvar* sv, FI
 	}
 	else if( sv->svtype == INVDUPRIGHT)
 	{
-		if( params->seq_resolved != 0)
+		if( sv->inner_start > sv->outer_start)
+			seq = readRefAltSeq( params, sv->chr_name, sv->outer_start, sv->inner_start);
+		else
+			seq = readRefAltSeq( params, sv->chr_name, sv->inner_start, sv->outer_start);
+
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
-			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, ".", ".", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, seq[0], seq, 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		}
+		else if( seq != NULL)
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, seq[0], "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		else
 			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, ".", "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 
+		if( seq != NULL)
+			free( seq);
+
 		invdup_cnt++;
 		sv_len = abs( ( sv->inner_start - sv->outer_start + 1));
 		total_invdup_length += sv_len;
 	}
 	else if( sv->svtype == INVDUPLEFT )
 	{
-		if( params->seq_resolved != 0)
+		if( sv->outer_end > sv->inner_end)
+			seq = readRefAltSeq( params, sv->chr_name, sv->inner_end, sv->outer_end);
+		else
+			seq = readRefAltSeq( params, sv->chr_name, sv->outer_end, sv->inner_end);
+
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
-			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, ".", ".", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, seq[0], seq, 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		}
+		else if( seq != NULL)
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, seq[0], "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		else
 			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, ".", "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 
+		if( seq != NULL)
+			free( seq);
+
 		invdup_cnt++;
 		sv_len = abs( ( sv->inner_end - sv->outer_end + 1));
 		total_invdup_length += sv_len;
 	}
 	else if( sv->svtype == INTERDUPRIGHT)
 	{
-		if( params->seq_resolved != 0)
+		if( sv->inner_start > sv->outer_start)
+			seq = readRefAltSeq( params, sv->chr_name, sv->outer_start, sv->inner_start);
+		else
+			seq = readRefAltSeq( params, sv->chr_name, sv->inner_start, sv->outer_start);
+
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
-			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, ".", ".", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, seq[0], seq, 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		}
+		else if( seq!= NULL)
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, seq[0], "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		else
 			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->outer_start) + 1," vh_dup_", ++dup_cnt, ".", "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 
+		if( seq != NULL)
+			free( seq);
+
 		interdup_cnt++;
 		sv_len = abs( ( sv->inner_start - sv->outer_start + 1));
 		total_interdup_length += sv_len;
 	}
 	else if( sv->svtype == INTERDUPLEFT )
 	{
-		if( params->seq_resolved != 0)
+		if( sv->outer_end > sv->inner_end)
+			seq = readRefAltSeq( params, sv->chr_name, sv->inner_end, sv->outer_end);
+		else
+			seq = readRefAltSeq( params, sv->chr_name, sv->outer_end, sv->inner_end);
+
+		if( ( params->seq_resolved != 0 || sv->imprecise == NOT_IMPRECISE) && seq != NULL)
 		{
-			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, ".", ".", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, seq[0], seq, 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		}
+		else if( seq != NULL)
+			fprintf( fpOut,"%s\t%i\t%s%d\t%c\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, seq[0], "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 		else
 			fprintf( fpOut,"%s\t%i\t%s%d\t%s\t%s%s%s\t%d\t%s\t", sv->chr_name, ( sv->inner_end) + 1," vh_dup_", ++dup_cnt, ".", "<", "DUP:ISP", ">", 255, ( sv->filtered == false) ? "PASS" : "LowQual");
 
+		if( seq != NULL)
+			free( seq);
+
 		interdup_cnt++;
 		sv_len = abs( ( sv->inner_end - sv->outer_end + 1));
 		total_interdup_length += sv_len;
diff --git a/vh/vh_divethandler.c b/vh/vh_divethandler.c
index a26763e..1540a92 100644
--- a/vh/vh_divethandler.c
+++ b/vh/vh_divethandler.c
@@ -371,9 +371,9 @@ DivetRow *vh_loadDivetRowFromBamAlternative( alternativeMapping *discordantReadP
 
 
 	//fprintf( divet_file, "%s\t%s\t%d\t%d\t%c\t=\t%d\t%d\t%c\t%c\t%d\t%d\t%d\n", discordantReadPtr->readName, discordantReadPtr->chromosome_name,
-		//	discordantReadPtr->pos1, discordantReadPtr->pos1_End, orientLeft, discordantReadPtr->pos2,
-			//discordantReadPtr->pos2_End, orientRight, SV, discordantReadPtr->editDistance,
-			//discordantReadPtr->mQual1, discordantReadPtr->mQual2);
+	//	discordantReadPtr->pos1, discordantReadPtr->pos1_End, orientLeft, discordantReadPtr->pos2,
+	//discordantReadPtr->pos2_End, orientRight, SV, discordantReadPtr->editDistance,
+	//discordantReadPtr->mQual1, discordantReadPtr->mQual2);
 
 	DivetRow *newRow = createDivetRowNew (libInfo->hash, discordantReadPtr->ten_x_barcode,
 			discordantReadPtr->readName, discordantReadPtr->chromosome_name, discordantReadPtr->pos1,
@@ -515,8 +515,8 @@ int read_Divet_bam( discordantMapping **mapping, parameters *params, LibraryInfo
 		while( discordantReadPtr != NULL)
 		{
 			is_satellite = sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name , discordantReadPtr->pos1, discordantReadPtr->pos1_End)
-		    					+ sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name, discordantReadPtr->pos2, discordantReadPtr->pos2_End)
-								+ sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name , discordantReadPtr->pos2, discordantReadPtr->pos2_End);
+		    									+ sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name, discordantReadPtr->pos2, discordantReadPtr->pos2_End)
+												+ sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name , discordantReadPtr->pos2, discordantReadPtr->pos2_End);
 
 			if ( is_satellite == 0 && discordantReadPtr->mQual1 > params->mq_threshold && discordantReadPtr->mQual2 > params->mq_threshold
 					&& !sonic_is_gap( params->this_sonic, params->this_sonic->chromosome_names[chr_index], discordantReadPtr->pos1, discordantReadPtr->pos2)
@@ -626,9 +626,9 @@ int read_Divet_bam_alternative( alternativeMapping **mapping, parameters *params
 			/* Since MT is circular, we need to eliminate the read-pairs at both ends of the chromosome */
 			insLen = abs( discordantReadPtr->pos1 - discordantReadPtr->pos2);
 			is_satellite = sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name , discordantReadPtr->pos1, discordantReadPtr->pos1_End)
-																											  + sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name, discordantReadPtr->pos2, discordantReadPtr->pos2_End)
-																											  + sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name , discordantReadPtr->pos2, discordantReadPtr->pos2_End)
-																											  + sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name, discordantReadPtr->pos2, discordantReadPtr->pos2_End);
+																															  + sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name, discordantReadPtr->pos2, discordantReadPtr->pos2_End)
+																															  + sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name , discordantReadPtr->pos2, discordantReadPtr->pos2_End)
+																															  + sonic_is_satellite( params->this_sonic, discordantReadPtr->chromosome_name, discordantReadPtr->pos2, discordantReadPtr->pos2_End);
 
 			if ( is_satellite == 0 && ( discordantReadPtr->mQual1 > params->mq_threshold) &&
 					( !sonic_is_gap( params->this_sonic, params->this_sonic->chromosome_names[chr_index], discordantReadPtr->pos1, discordantReadPtr->pos2)) &&
@@ -826,13 +826,13 @@ int load_Divet_bam( bam_info** in_bams, parameters *params, int chr_index)
 	g_maxListBrkPointIntr = MAXLISTBRKPOINTINTR;
 	g_libInfo = NULL;
 
-/*
+	/*
 	divetfile_path = (char *) getMem(sizeof(char) * (2+strlen("divv.vh")+strlen(params->outprefix)));
 	sprintf(divetfile_path, "%s-%s", params->outprefix, "divv.vh");
 
 	divet_file = safe_fopen (divetfile_path, "w");
 	free(divetfile_path);
-	*/
+	 */
 
 	del_cnt_div = 0, ins_cnt_div = 0, inv_cnt_div = 0, tandup_cnt_div = 0, sr_cnt_div = 0, alt_cnt_div = 0, invdup_cnt_div = 0, interdup_cnt_div = 0;
 
@@ -840,6 +840,9 @@ int load_Divet_bam( bam_info** in_bams, parameters *params, int chr_index)
 	{
 		for( lib_cnt = 0; lib_cnt < in_bams[bam_index]->num_libraries; lib_cnt++)
 		{
+			if( in_bams[bam_index]->libraries[lib_cnt]->is_valid == false)
+				continue;
+
 			newLibInfo = ( struct LibraryInfo *) getMem( sizeof( struct LibraryInfo));
 			strcpy( newLibInfo->libName, in_bams[bam_index]->libraries[lib_cnt]->libname);
 			strcpy( newLibInfo->indName, in_bams[bam_index]->sample_name);
@@ -882,6 +885,9 @@ int load_Divet_bam( bam_info** in_bams, parameters *params, int chr_index)
 		{
 			for( lib_cnt = 0; lib_cnt < in_bams[bam_index]->num_libraries; lib_cnt++)
 			{
+				if( in_bams[bam_index]->libraries[lib_cnt]->is_valid == false)
+					continue;
+
 				newLibInfo = ( struct LibraryInfo *) getMem( sizeof( struct LibraryInfo));
 				strcpy( newLibInfo->libName, "Alternative\0");
 				strcpy( newLibInfo->indName, in_bams[bam_index]->sample_name);
@@ -926,6 +932,9 @@ int load_Divet_bam( bam_info** in_bams, parameters *params, int chr_index)
 		{
 			for( lib_cnt = 0; lib_cnt < in_bams[bam_index]->num_libraries; lib_cnt++)
 			{
+				if( in_bams[bam_index]->libraries[lib_cnt]->is_valid == false)
+					continue;
+
 				newLibInfo = ( struct LibraryInfo *) getMem( sizeof( struct LibraryInfo));
 				strcpy( newLibInfo->libName, "SplitRead\0");
 				strcpy( newLibInfo->indName, in_bams[bam_index]->sample_name);