diff --git a/src/VIVA.jl b/src/VIVA.jl
index a541256..49f73c9 100644
--- a/src/VIVA.jl
+++ b/src/VIVA.jl
@@ -17,13 +17,6 @@ using Test
 
 #end #module
 
-#=
-const g_white = "400" #homo reference 0/0
-const g_red = "800" #homo variant 1/1 1/2 2/2 1/3 2/3 3/3 4/4 5/5 6/6 etc
-const g_pink = "600" #hetero variant 0/1 1/0 0/2 2/0 etc
-const g_blue = "0" #no call ./.
-=#
-
 export
     format_reader,
     load_vcf,
@@ -80,8 +73,7 @@ export
     add_pheno_matrix_to_dp_data_for_plotting,
     generate_hover_text_array,
     generate_hover_text_array_grouped,
-    save_graphic,
-    alias
+    save_graphic
 
 #include("vcf_utils.jl")
 include("vcf_utils_complete.jl")
diff --git a/src/vcf_utils_complete.jl b/src/vcf_utils_complete.jl
index a46ac52..1f9f6b0 100644
--- a/src/vcf_utils_complete.jl
+++ b/src/vcf_utils_complete.jl
@@ -17,7 +17,7 @@ end
 
 """
     clean_column1_siglist!(siglist)
-    replaces "X","Y","M" with 23,24,25 {Int}
+Replaces strings "X","Y","M" with 23,24,25 {Int} in array generated in load_siglist()
 use in load_siglist() because X and Y need to be replaced with Int
 """
 function clean_column1_siglist!(siglist)
@@ -1476,13 +1476,15 @@ return(hover_text_array)
 end
 
 """
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 Save plot in either html or static image formats incuding eps, png, svg, and pdf
 """
-function save_graphic(graphic,output_directory,save_ext,title)
+function save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
-    if save_ext=="html"
+    if save_ext=="html" && remote_option == true
         PlotlyJS.savehtml(graphic, joinpath("$(output_directory)" ,"$title.$(save_ext)"), :remote)
+    elseif save_ext=="html" && remote_option != true
+        PlotlyJS.savehtml(graphic, joinpath("$(output_directory)" ,"$title.$(save_ext)"))
     elseif save_ext != "html"
         PlotlyJS.savefig(graphic, joinpath("$(output_directory)" ,"$title.$(save_ext)"))
     end
diff --git a/test/.DS_Store b/test/.DS_Store
index 058d747..81c6827 100644
Binary files a/test/.DS_Store and b/test/.DS_Store differ
diff --git a/test/new_vcf_utils.jl b/test/new_vcf_utils.jl
index 5a7b51a..95f773c 100644
--- a/test/new_vcf_utils.jl
+++ b/test/new_vcf_utils.jl
@@ -12,10 +12,10 @@ julia> Pkg.test(pkg_for"VIVA")
 @testset "VCFUtils" begin
 
 vcf_filename = "test_files/test_4X_191.vcf"
-vcf_filename_with_chr = "test_files/test_with_chr.vcf"
+#vcf_filename_with_chr = "test_files/test_with_chr.vcf"
 
 reader = VCF.Reader(open(vcf_filename, "r"))
-reader_with_chr = VCF.Reader(open(vcf_filename_with_chr, "r"))
+#reader_with_chr = VCF.Reader(open(vcf_filename_with_chr, "r"))
 sample_names = get_sample_names(reader)
 
 dp_limit = 50
@@ -30,23 +30,23 @@ end
 
 #functions for variant filters
 
-@testset "io_chromosome_range_vcf_filter" begin
-sub = io_chromosome_range_vcf_filter("chr4:0-400000000",vcf_filename)
+@testset "io_genomic_range_vcf_filter" begin
+sub = io_genomic_range_vcf_filter("chr4:0-400000000",vcf_filename)
 @test typeof(sub) == Array{Any,1}
 @test size(sub,1) == 1012
-#println("io_chromosome_range_vcf_filter type is $(typeof(sub))")
-#println("io_chromosome_range_vcf_filter size is $(size(sub,1))")
+#println("io_genomic_range_vcf_filter type is $(typeof(sub))")
+#println("io_genomic_range_vcf_filter size is $(size(sub,1))")
 end
 
 
 @testset "filters_with_siglist" begin
 
     @testset "load_siglist" begin
-    sig_list=load_siglist("test_files/sig_list_for_test.csv")
+    sig_list=load_siglist("test_files/positions_list.csv")
 
-    @testset "pass_chrrange_siglist_filter" begin
-    sig_list=load_siglist("test_files/sig_list_for_test.csv")
-    sub = pass_chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-5000000000")
+    @testset "pass_genomic_range_siglist_filter" begin
+    sig_list=load_siglist("test_files/positions_list.csv")
+    sub = pass_genomic_range_siglist_filter(vcf_filename,sig_list,"chr4:0-5000000000")
 
     @test (typeof(sub[1])) == GeneticVariation.VCF.Record
     @test (length(sub)) ==  5
@@ -66,8 +66,8 @@ end
             @test (length(sub)) ==  10
             end
 
-            @testset "chrrange_siglist_filter" begin
-            sub = chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
+            @testset "genomic_range_siglist_filter" begin
+            sub = genomic_range_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
             @test (typeof(sub[1])) == GeneticVariation.VCF.Record
             @test (length(sub)) ==  5
             end
@@ -82,9 +82,9 @@ end
     @test (length(sub)) ==  1164
 end
 
-@testset "pass_chrrange_filter" begin
+@testset "pass_genomic_range_filter" begin
     reader = VCF.Reader(open(vcf_filename, "r"))
-    sub = pass_chrrange_filter(reader,"chr4:0-400000000",vcf_filename)
+    sub = pass_genomic_range_filter(reader,"chr4:0-400000000",vcf_filename)
     @test (typeof(sub[1])) == GeneticVariation.VCF.Record
     @test (length(sub)) ==  856
 end
@@ -220,7 +220,7 @@ dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
     end
 
     @testset "sortcols_by_phenotype_matrix" begin
-    vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/fixed_pheno_matrix_test.csv","case,control", dp_num_array, sample_names)
+    vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/sample_metadata_matrix.csv","case,control", dp_num_array, sample_names)
     #println("sortcols_by_phenotype_matrix vcf type is $(typeof(vcf))")
     #println("sortcols_by_phenotype_matrix vcf size is $(size(vcf,1))")
     #println("sortcols_by_phenotype_matrix group_label_pack type is $(typeof(group_label_pack))")
diff --git a/test/test_files/test_with_chr.vcf b/test/test_files/chr_format.vcf
similarity index 100%
rename from test/test_files/test_with_chr.vcf
rename to test/test_files/chr_format.vcf
diff --git a/test/test_files/pheno_matrix_chr.csv b/test/test_files/pheno_matrix_chr.csv
deleted file mode 100644
index 61124fa..0000000
--- a/test/test_files/pheno_matrix_chr.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-id,WESPE2004,WESPE2006,WESPE2008,WESPE2037,WESPE2056,WESPE2058,WESPE2066,WESPE2105,WESPE2115,WESPE2120,WESPE2159,WESPE2161,WESPE2201,WESPE2253,WESPE2260,WESPE2287,WESPE2295,WESPE2310,WESPE2311,WESPE2314,WESPE2324,WESPE2333,WESPE2362,WESPE2370,WESPE2385,WESPE2388,WESPE2390,WESPE2415,WESPE2418,WESPE2437,WESPE2480,WESPE2486,WESPE2496,WESPE2523,WESPE2530,WESPE2531,WESPE2545,WESPE2555,WESPE2579,WESPE2621,WESPE2633,WESPE2705,WESPE2757,WESPE2782,WESPE2829,WESPE2844,WESPE2851,WESPE2876,WESPE2925,WESPE2932,wespe2007,wespe2020,wespe2023,wespe2051,wespe2074,wespe2079,wespe2084,wespe2141,wespe2182,wespe2185,wespe2233,wespe2234,wespe2257,wespe2291,wespe2307,wespe2325,wespe2334,wespe2346,wespe2354,wespe2358,wespe2366,wespe2407,wespe2432,wespe2440,wespe2463,wespe2482,wespe2483,wespe2488,wespe2518,wespe2525,wespe2543,wespe2567,wespe2602,wespe2611,wespe2638,wespe2645,wespe2662,wespe2670,wespe2727,wespe2744,wespe2776,wespe2812,wespe2840,wespe2877,wespe2889,wespe2896,wespe2908,wespe2912,wespe2946,wespe2980
-"test1,test2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
\ No newline at end of file
diff --git a/test/test_files/sig_list_for_test.csv b/test/test_files/positions_list.csv
similarity index 100%
rename from test/test_files/sig_list_for_test.csv
rename to test/test_files/positions_list.csv
diff --git a/test/test_files/positions_list_test_4X_191.csv b/test/test_files/positions_list_test_4X_191.csv
deleted file mode 100644
index 9541902..0000000
--- a/test/test_files/positions_list_test_4X_191.csv
+++ /dev/null
@@ -1,16 +0,0 @@
-Chr,Start
-4,3162034
-4,3162056
-4,3162170
-X,46460089
-X,46460615
-X,46460899
-X,46461449
-X,46461486
-X,46461536
-X,46462031
-X,46462132
-4,3076380
-4,3076381
-4,3076384
-4,3076390
\ No newline at end of file
diff --git a/test/test_files/fixed_pheno_matrix_test.csv b/test/test_files/sample_metadata_matrix.csv
similarity index 100%
rename from test/test_files/fixed_pheno_matrix_test.csv
rename to test/test_files/sample_metadata_matrix.csv
diff --git a/test/test_files/sample_order_list_fortest.txt b/test/test_files/sample_order_list_fortest.txt
deleted file mode 100644
index b0281c2..0000000
--- a/test/test_files/sample_order_list_fortest.txt
+++ /dev/null
@@ -1 +0,0 @@
-_CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	addrg_dedup_Lib2_16.bam	addrg_dedup_Lib2_2.bam	addrg_dedup_Lib2_4.bam	addrg_dedup_Lib2_7.bam	addrg_dedup_Lib1_12.bam	addrg_dedup_Lib1_19.bam	addrg_dedup_Lib1_5.bam	addrg_dedup_Lib1_6.bam	addrg_dedup_Lib3_13.bam	addrg_dedup_Lib3_14.bam	addrg_dedup_Lib3_15.bam	addrg_dedup_Lib3_18.bam	addrg_dedup_Lib4_1.bam	addrg_dedup_Lib4_10.bam	addrg_dedup_Lib4_11.bam	addrg_dedup_Lib4_8.bam	addrg_dedup_Lib5_22.bam	addrg_dedup_Lib5_27.bam	addrg_dedup_Lib5_3.bam	addrg_dedup_Lib5_9.bam	addrg_dedup_Lib6_20.bam	addrg_dedup_Lib6_21.bam	addrg_dedup_Lib6_23.bam	addrg_dedup_Lib6_25.bam
\ No newline at end of file
diff --git a/test/test_files/sample_phenotype_matrix.csv b/test/test_files/sample_phenotype_matrix.csv
deleted file mode 100644
index 0763bab..0000000
--- a/test/test_files/sample_phenotype_matrix.csv
+++ /dev/null
@@ -1,4 +0,0 @@
-id,MODcas1001,MODcas1003,MODcas1005,MODcas1010,MODcas1012,MODcas1013,MODcas1014,MODcas1015,MODcas1017,MODcas1018,MODcas1019,MODcas1020,MODcas1021,MODcas1022,MODcas1023,MODcas1024,MODcas2025,MODcas2027,MODcas2028,MODcas2029,MODcas2032,MODcas2033,MODcas2034,MODcas2035,MODcas2038,MODcas2039,MODcas2040,MODcas2041,MODcas2043,MODcas2044,MODcas2045,MODcas2048,MODcas3050,MODcas3051,MODcas3052,MODcas3053,MODcas3054,MODcas3055,MODcas3056,MODcas3057,MODcas3058,MODcas3059,MODcas3060,MODcas3061,MODcas3062,MODcas3065,MODcas3072,MODcas3073,MODcas3074,MODcas3075,MODcas3076,MODcas3077,MODcas3078,MODcas3079,MODcas3080,MODcas3081,MODcas3082,MODcas3083,MODcas3084,MODcas3085,MODcas3086,MODcas3089,MODcas3092,MODcas3096,MODcon1002,MODcon1004,MODcon1006,MODcon1007,MODcon1008,MODcon1009,MODcon1011,MODcon1016,MODcon2026,MODcon2030,MODcon2031,MODcon2036,MODcon2037,MODcon2042,MODcon2046,MODcon2047,MODcon3063,MODcon3064,MODcon3066,MODcon3067,MODcon3068,MODcon3069,MODcon3070,MODcon3071,MODcon3087,MODcon3088,MODcon3090,MODcon3091,MODcon3093,MODcon3094,MODcon3095,MODcas4097,MODcas4098,MODcas4099,MODcas4100,MODcas4101,MODcas4102,MODcas4103,MODcas4104,MODcas4105,MODcas4106,MODcas4107,MODcas4108,MODcas4111,MODcas4112,MODcas4115,MODcas4116,MODcas4123,MODcas4124,MODcas4127,MODcas4128,MODcas4133,MODcas4134,MODcas4135,MODcas4136,MODcas4137,MODcas4138,MODcas4139,MODcas4140,MODcas4141,MODcas4142,MODcas4143,MODcas4144,MODcas5145,MODcas5147,MODcas5150,MODcas5152,MODcas5153,MODcas5154,MODcas5155,MODcas5156,MODcas5162,MODcas5163,MODcas5164,MODcas5166,MODcas5168,MODcas5169,MODcas5170,MODcas5173,MODcas5176,MODcas5177,MODcas5178,MODcas5179,MODcas5180,MODcas5181,MODcas5183,MODcas5184,MODcas5185,MODcas5186,MODcas5187,MODcas5188,MODcas5189,MODcas5190,MODcas5191,MODcas5192,MODcon4109,MODcon4110,MODcon4113,MODcon4114,MODcon4117,MODcon4118,MODcon4119,MODcon4120,MODcon4121,MODcon4122,MODcon4125,MODcon4126,MODcon4129,MODcon4130,MODcon4131,MODcon4132,MODcon5146,MODcon5148,MODcon5149,MODcon5151,MODcon5157,MODcon5158,MODcon5159,MODcon5160,MODcon5161,MODcon5165,MODcon5167,MODcon5171,MODcon5172,MODcon5174,MODcon5175,MODcon5182
-"seq1,seq2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
-"sequencing_site_1,sequencing_site_2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
-"test1,test2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
diff --git a/test/test_files/select_samples_list.txt b/test/test_files/select_samples_list.txt
index 1c6f186..920b15c 100644
--- a/test/test_files/select_samples_list.txt
+++ b/test/test_files/select_samples_list.txt
@@ -1 +1 @@
-cas1001	cas1003	cas1005	cas1010	cas1012
+cas1001	cas1003	cas1005	cas1010	cas1012
\ No newline at end of file
diff --git a/test/test_files/sig_list_50.csv b/test/test_files/sig_list_50.csv
deleted file mode 100644
index 52f9d82..0000000
--- a/test/test_files/sig_list_50.csv
+++ /dev/null
@@ -1,477 +0,0 @@
-Chr,Start
-chr1,865584
-chr1,865625
-chr1,865694
-chr1,887799
-chr1,889403
-chr1,949781
-chr1,1019513
-chr1,1115644
-chr1,1141824
-chr1,1168310
-chr1,1222895
-chr1,1222958
-chr1,1231280
-chr1,1245176
-chr1,1254483
-chr1,1262635
-chr1,1262958
-chr1,1275810
-chr1,1289446
-chr1,1391656
-chr1,1425753
-chr1,1431075
-chr1,1459235
-chr1,1847886
-chr1,1847952
-chr1,2075740
-chr1,2129498
-chr1,2252970
-chr1,2290143
-chr1,2411250
-chr1,2451384
-chr1,2524107
-chr1,2938887
-chr1,2938924
-chr1,3342635
-chr1,3389757
-chr1,3394464
-chr1,3424388
-chr1,3519162
-chr1,3551737
-chr1,3732885
-chr1,3807359
-chr1,3807590
-chr1,3809544
-chr1,5923427
-chr1,5923462
-chr1,5934652
-chr1,5940243
-chr1,5950975
-chr1,5965455
-chr1,6008178
-chr1,6046264
-chr1,6273206
-chr1,6304454
-chr1,6354992
-chr1,6528302
-chr1,6534643
-chr1,6615539
-chr1,6636662
-chr1,6637055
-chr1,6741027
-chr1,8075424
-chr1,9075221
-chr1,9097830
-chr1,9165669
-chr1,9307032
-chr1,9322376
-chr1,9324338
-chr1,9673046
-chr1,9714365
-chr1,9811653
-chr1,10316344
-chr1,10364385
-chr1,10394627
-chr1,10397567
-chr1,10521629
-chr1,10521657
-chr1,10523133
-chr1,10715845
-chr1,10725391
-chr1,10725413
-chr1,11009844
-chr1,11105539
-chr1,11106642
-chr1,11106666
-chr1,11106756
-chr1,11253684
-chr1,11561257
-chr1,11561489
-chr1,11766740
-chr1,11771929
-chr1,11772427
-chr1,11844424
-chr1,11852412
-chr1,11894340
-chr1,11983352
-chr1,12025600
-chr1,12027051
-chr1,12175658
-chr1,12202555
-chr1,12266982
-chr1,12309344
-chr1,12336265
-chr1,12423276
-chr1,12785295
-chr1,12819343
-chr1,12820808
-chr1,12919067
-chr1,14109023
-chr1,14109122
-chr1,15793937
-chr1,15850579
-chr1,16064670
-chr1,16069612
-chr1,16070820
-chr1,16071015
-chr1,16071058
-chr1,16255205
-chr1,16456763
-chr1,16461581
-chr1,16464612
-chr1,16531299
-chr1,16721628
-chr1,16736327
-chr1,16785378
-chr1,17250898
-chr1,17256491
-chr1,17256626
-chr1,17263214
-chr1,17263229
-chr1,17265416
-chr1,17270653
-chr1,17295659
-chr1,17323602
-chr1,17332012
-chr1,17420146
-chr1,17567149
-chr1,17570691
-chr1,17588689
-chr1,17607274
-chr1,17668888
-chr1,17681163
-chr1,17764914
-chr1,18023699
-chr1,18023729
-chr1,18152646
-chr1,18807521
-chr1,19166151
-chr1,19199448
-chr1,19500103
-chr1,19565736
-chr1,19600406
-chr1,20072108
-chr1,20073703
-chr1,20082247
-chr1,20442878
-chr1,20640926
-chr1,20644156
-chr1,20645086
-chr1,20998508
-chr1,21048472
-chr1,21050719
-chr1,21155679
-chr1,21180098
-chr1,22182115
-chr1,22199175
-chr1,22200947
-chr1,22202856
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diff --git a/test/test_files/test_sample_phenotype_matrix.csv b/test/test_files/test_sample_phenotype_matrix.csv
deleted file mode 100644
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+++ /dev/null
@@ -1,4 +0,0 @@
-id,cas1001,cas1003,cas1005,cas1010,cas1012,cas1013,cas1014,cas1015,cas1017,cas1018,cas1019,cas1020,cas1021,cas1022,cas1023,cas1024,cas2025,cas2027,cas2028,cas2029,cas2032,cas2033,cas2034,cas2035,cas2038,cas2039,cas2040,cas2041,cas2043,cas2044,cas2045,cas2048,cas3050,cas3051,cas3052,cas3053,cas3054,cas3055,cas3056,cas3057,cas3058,cas3059,cas3060,cas3061,cas3062,cas3065,cas3072,cas3073,cas3074,cas3075,cas3076,cas3077,cas3078,cas3079,cas3080,cas3081,cas3082,cas3083,cas3084,cas3085,cas3086,cas3089,cas3092,cas3096,con1002,con1004,con1006,con1007,con1008,con1009,con1011,con1016,con2026,con2030,con2031,con2036,con2037,con2042,con2046,con2047,con3063,con3064,con3066,con3067,con3068,con3069,con3070,con3071,con3087,con3088,con3090,con3091,con3093,con3094,con3095,cas4097,cas4098,cas4099,cas4100,cas4101,cas4102,cas4103,cas4104,cas4105,cas4106,cas4107,cas4108,cas4111,cas4112,cas4115,cas4116,cas4123,cas4124,cas4127,cas4128,cas4133,cas4134,cas4135,cas4136,cas4137,cas4138,cas4139,cas4140,cas4141,cas4142,cas4143,cas4144,cas5145,cas5147,cas5150,cas5152,cas5153,cas5154,cas5155,cas5156,cas5162,cas5163,cas5164,cas5166,cas5168,cas5169,cas5170,cas5173,cas5176,cas5177,cas5178,cas5179,cas5180,cas5181,cas5183,cas5184,cas5185,cas5186,cas5187,cas5188,cas5189,cas5190,cas5191,cas5192,con4109,con4110,con4113,con4114,con4117,con4118,con4119,con4120,con4121,con4122,con4125,con4126,con4129,con4130,con4131,con4132,con5146,con5148,con5149,con5151,con5157,con5158,con5159,con5160,con5161,con5165,con5167,con5171,con5172,con5174,con5175,con5182
-"seq1,seq2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
-"sequencing_site_1,sequencing_site_2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1
-"test1,test2",1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2
\ No newline at end of file
diff --git a/viva b/viva
index 79ec1b4..3572997 100755
--- a/viva
+++ b/viva
@@ -54,12 +54,11 @@ function test_parse_main(ARGS::Vector{String})
         default = "html"
 
         "--genomic_range", "-r"
-        help = "select rows within a given chromosome range. Provide chromosome range after this flag."
+        help = "select rows within a given chromosome range. Provide chromosome range after this flag in format chr4:20000000-30000000."
         arg_type = String
 
         "--pass_filter", "-p"
-        help = "select rows within a given chromosome range. Provide chromosome range after this flag in format chr4:20000000-30000000"
-        arg_type = String
+        help = "select rows with PASS in the FILTER field."
         action = :store_true
 
         "--positions_list", "-l"
@@ -99,6 +98,12 @@ function test_parse_main(ARGS::Vector{String})
 
         "--avg_dp"
         help = "visualize average read depths as line chart. Options: average sample read depth, average variant read depth, or both. eg. =sample, =variant, =sample,variant"
+
+        "--save_remotely"
+        help = "Specify filename for heatmap with underscores for spaces."
+        action = :store_true
+
+
         #nargs = 2
         #metavar = ["avg_option", "markers_or_lines"]
         #default = ["variant,sample", "markers"]
@@ -134,6 +139,8 @@ sample_names = get_sample_names(reader)
 
 save_ext = parsed_args["save_format"]
 
+remote_option = parsed_args["save_remotely"]
+
 VIVA.checkfor_outputdirectory(parsed_args["output_directory"])
 output_directory=parsed_args["output_directory"]
 
@@ -311,7 +318,7 @@ if parsed_args["heatmap"] == "genotype"
 
     println("Saving genotype heatmap")
 
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
 end
 
@@ -379,7 +386,7 @@ if parsed_args["heatmap"] == "read_depth"
 
     println("Saving read depth heatmap")
 
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 end
 
 if parsed_args["heatmap"] == "genotype,read_depth" || parsed_args["heatmap"] == "read_depth,genotype"
@@ -448,7 +455,7 @@ if parsed_args["heatmap"] == "genotype,read_depth" || parsed_args["heatmap"] ==
     save_numerical_array(gt_num_array,sample_names,chr_pos_tuple_list,title,output_directory)
     end
 
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
     if parsed_args["heatmap_title"] != nothing
         title = "Read_Depth_$(parsed_args["heatmap_title"])"
@@ -509,7 +516,7 @@ if parsed_args["heatmap"] == "genotype,read_depth" || parsed_args["heatmap"] ==
 
     println("Saving read depth heatmap")
 
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
 end
 
@@ -530,7 +537,7 @@ if parsed_args["avg_dp"] == "sample"
     bn = Base.Filesystem.basename(parsed_args["vcf_file"])
     title = "Average_Sample_Read_Depth_$bn"
 
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
 elseif parsed_args["avg_dp"] == "variant"
 
@@ -550,7 +557,7 @@ elseif parsed_args["avg_dp"] == "variant"
     title = "Average_Variant_Read_Depth$bn"
 
     graphic = avg_variant_dp_line_chart(avg_list,chr_pos_tuple_list,y_axis_label_option,chrom_label_info)
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
 elseif parsed_args["avg_dp"] == "variant,sample" || parsed_args["avg_dp"] == "sample,variant"
 
@@ -570,7 +577,7 @@ elseif parsed_args["avg_dp"] == "variant,sample" || parsed_args["avg_dp"] == "sa
     title = "Average_Variant_Read_Depth$bn"
 
     graphic = avg_variant_dp_line_chart(avg_list,chr_pos_tuple_list,y_axis_label_option,chrom_label_info)
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
     avg_list = VIVA.avg_dp_samples(dp_num_array)
     list = VIVA.list_sample_names_low_dp(avg_list, sample_names)
@@ -582,7 +589,7 @@ elseif parsed_args["avg_dp"] == "variant,sample" || parsed_args["avg_dp"] == "sa
 
     graphic = avg_sample_dp_scatter(avg_list,sample_names,x_axis_label_option)
 
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
 elseif parsed_args["avg_dp"] != nothing
     println("--avg_dp flag did not find expected arguments: sample, variant, or sample,variant. Average read depth plot not saved.")