--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test3.ini	Wed Jan 08 09:15:19 2020 -0500
@@ -0,0 +1,167 @@
+[x-axis]
+where = top
+[hic_section_0_0]
+file = test-data/Li_et_al_2015.h5
+file_type = hic_matrix
+title = Kc DpnII (Li et al. 2015) log1p
+depth = 200000
+colormap = RdYlBu_r
+transform = log1p
+scale_factor = 1.0
+rasterize = true
+[tads_0_0]
+file = test-data/domains.bed
+file_type = domains
+border_color = black
+color = none
+overlay_previous = share-y
+[chrom states_1]
+file = test-data/tad_classification.bed
+title = TAD state
+color = bed_rgb
+border_color = #000000
+display = collapsed
+height = 0.5
+line_width = 0.5
+file_type = bed
+[hic_section_2_0]
+file = test-data/Li_et_al_2015.h5
+file_type = hic_matrix
+title = Kc DpnII (Li et al. 2015) inverted no transform
+depth = 200000
+colormap = Reds
+min_value = 5.0
+max_value = 70.0
+orientation = inverted
+scale_factor = 1.0
+rasterize = true
+[spacer]
+height = 1.0
+[bedgraph_4]
+file = test-data/test_with_neg_values.bg.gz
+title = bedgraph with negative values
+color = black
+alpha = 1.0
+negative_color = red
+height = 4.0
+show_data_range = false
+nans_to_zeros = false
+use_middle = false
+file_type = bedgraph
+type = fill
+overlay_previous = no
+[bedgraph_5]
+file = test-data/bedgraph_chrx_2e6_5e6.bg
+title = bedgraph
+color = blue
+alpha = 1.0
+height = 4.0
+show_data_range = false
+nans_to_zeros = false
+use_middle = false
+file_type = bedgraph
+type = fill
+overlay_previous = no
+[bigwig_6]
+file = test-data/bigwig_chrx_2e6_5e6.bw
+title = rep 1 test fill
+color = blue
+alpha = 1.0
+height = 4.0
+summary_method = mean
+nans_to_zeros = false
+type = fill
+show_data_range = false
+file_type = bigwig
+overlay_previous = no
+[bigwig_7]
+file = test-data/bigwig_chrx_2e6_5e6.bw
+title = (red points/width=5/max value/100 bins) overlayed with (dark red line/min value/30000 bins) overlayed with (black line/min value)
+color = red
+alpha = 1.0
+height = 10.0
+summary_method = max
+nans_to_zeros = false
+number_of_bins = 100
+type = points:5.0
+show_data_range = false
+file_type = bigwig
+overlay_previous = no
+[bigwig_8]
+file = test-data/bigwig_chrx_2e6_5e6.bw
+color = #c00000
+alpha = 1.0
+height = 10.0
+summary_method = min
+nans_to_zeros = false
+type = line:0.5
+show_data_range = false
+file_type = bigwig
+overlay_previous = share-y
+[bigwig_9]
+file = test-data/bigwig_chrx_2e6_5e6.bw
+color = black
+alpha = 1.0
+height = 10.0
+summary_method = min
+nans_to_zeros = false
+number_of_bins = 30000
+type = line:0.5
+show_data_range = false
+file_type = bigwig
+overlay_previous = share-y
+[spacer]
+height = 1.0
+[genes_10_0]
+file = test-data/dm3_genes.bed.gz
+title = genes in ucsc
+color = #000000
+border_color = #000000
+style = UCSC
+arrow_interval = 2
+display = stacked
+height = 5.0
+labels = true
+file_type = bed
+fontsize = 10
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
+[genes_11_0]
+file = test-data/dm3_genes.bed6.gz
+title = bed6 global max row color from score
+color = RdYlBu_r
+border_color = #000000
+style = flybase
+height_utr = 1.0
+color_utr = grey
+display = stacked
+height = 20.0
+labels = true
+file_type = bed
+fontsize = 10
+global_max_row = true
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
+[genes_12_0]
+file = test-data/domains.bed
+title = domains.bed using the 9th field for colors interleaved
+color = bed_rgb
+border_color = red
+style = flybase
+height_utr = 1.0
+color_utr = grey
+display = interleaved
+height = 2.0
+labels = false
+file_type = bed
+fontsize = 10
+global_max_row = false
+max_labels = 60
+line_width = 0.5
+arrowhead_included = false
+overlay_previous = no
\ No newline at end of file