#General
SESSION.RELATIVE_PATH	Use relative paths in session files	boolean
IGV.single.track.pane	Display all tracks in a single panel	boolean
IGV.track.show.attribute.views	Show attribute panel	boolean

FLANKING_REGION	Feature flanking region	integer	< 0 interpreted as a percentage

#Tracks 
IGV.chart.track.height	Default numeric track height (pixels)	integer
IGV.track.height	Default feature track height (pixels)	integer



//// IGNORE EVERYTHING BELOW HERE
  
    // UI behavior
 TOOLTIP.INITIAL_DELAY
 TOOLTIP.RESHOW_DELAY
 TOOLTIP.DISMISS_DELAY
 DEFAULT_FONT_SIZE
 DEFAULT_FONT_FAMILY
 DEFAULT_FONT_ATTRIBUTE
 ENABLE_ANTIALIASING
 SCALE_FONTS
 NAME_PANEL_WIDTH
 BACKGROUND_COLOR


 DETAILS_BEHAVIOR
 SKIP_VERSION
 SHOW_DEFAULT_TRACK_ATTRIBUTES
 SHOW_GENOME_SERVER_WARNING

    //
 IGV.Session.recent.sessions
 LAST_EXPORTED_REGION_DIRECTORY
 LAST_TRACK_DIRECTORY
 LAST_SNAPSHOT_DIRECTORY
 LAST_GENOME_IMPORT_DIRECTORY
 DEFINE_GENOME_INPUT_DIRECTORY_KEY
 DEFAULT_GENOME_KEY
 AUTO_UPDATE_GENOMES
 IGV.Bounds


 IGV.genome.sequence.dir
 BLAT_URL
 EXTVIEW_URL
 MASTER_RESOURCE_FILE_KEY

    // Search (go to) options
 SEARCH_ZOOM


    // Generic track options
 BYPASS_FILE_AUTO_DISCOVERY
 TRACK_ATTRIBUTE_NAME_KEY
 15
 COLOR_SCALE_

 CHART.SHOW_ALL_HEATMAP
 SHOW_REGION_BARS
 DEFAULT_VISIBILITY_WINDOW
 EXPAND_FEATURE_TRACKS
 IGV_PLUGIN_LIST
 SASHIMI.SHOW_COVERAGE
 GENE_LIST_BED_FORMAT

 SHOW_SIZE_WARNING

    // Chart (bar, heatmap, plots) options
 NORMALIZE_COVERAGE
 CHART.DRAW_TOP_BORDER
 CHART.DRAW_BOTTOM_BORDER
 CHART.COLOR_BORDERS
 CHART.DRAW_AXIS
 CHART.DRAW_TRACK_NAME
 CHART.COLOR_TRACK_NAME
 CHART.AUTOSCALE
 CHART.SHOW_DATA_RANGE

    // Alignment options
 SAM.ALLELE_THRESHOLD
 SAM.ALLELE_USE_QUALITY
 SAM.QUALITY_THRESHOLD
 SAM.COMPUTE_ISIZES
 SAM.INSERT_SIZE_THRESHOLD
 SAM.MIN_INSERT_SIZE_THRESHOLD
 SAM.ISIZE_MAX_PERCENTILE
 SAM.MIN_ISIZE_MIN_PERCENTILE
 SAM.AUTOSORT
 SAM.SHADE_CENTER
 SAM.SHOW_CENTER_LINE
 SAM.SHOW_REF_SEQ
 SAM.SHOW_COV_TRACK
 SAM.SHADE_BASE_QUALITY
 SAM.BASE_QUALITY_MIN
 SAM.BASE_QUALITY_MAX
 SAM.FILTER_ALIGNMENTS
 SAM.FILTER_SECONDARY_ALIGNMENTS
 SAM.FILTER_SUPPLEMENTARY_ALIGNMENTS
 SAM.FILTER_URL
 SAM.HIDDEN_TAGS
 SAM.MAX_VISIBLE_RANGE
 SAM.SHOW_DUPLICATES
 SAM.QUICK_CONSENSUS_MODE
 SAM.SHOW_SOFT_CLIPPED
 SAM.FLAG_UNMAPPED_PAIR
 SAM.MAX_LEVELS // Sampling count
 SAM.SAMPLING_WINDOW
 SAM.DOWNSAMPLE_READS
 SAM.SORT_OPTION
 SAM.GROUP_OPTION
 SAM.SHOW_ALL_BASES
 SAM.COLOR_BY
 SAM.COLOR_BY_TAG
 SAM.SORT_BY_TAG
 SAM.GROUP_BY_TAG
 SAM.GROUP_BY_POS
 SAM.BISULFITE_CONTEXT
 SAM.FILTER_FAILED_READS

 SAM.FLAG_ZERO_QUALITY
 SAM.SHOW_JUNCTION_TRACK
 SAM.JUNCTION_MIN_FLANKING_WIDTH
 SAM.JUNCTION_MIN_COVERAGE
 SAM.SHOW_INSERTION_INTERVALS
