text: #General
  SESSION.RELATIVE_PATH	Use relative paths in session files	boolean	TRUE
  IGV.single.track.pane	Display all tracks in a single panel	boolean	FALSE
  IGV.track.show.attribute.views	Show attribute panel	boolean	FALSE
  SHOW_DEFAULT_TRACK_ATTRIBUTES	Show default track attributes	boolean	FALSE
  SHOW_REGION_BARS	Show region-of-interest boundaries	boolean	FALSE
  ENABLE_GOOGLE_MENU	Enable Google access	boolean	FALSE	Enable loading from Google apis.
  FLANKING_REGION	Feature flanking region	integer	2000	< 0 interpreted as a percentage.
  DEFAULT_VISIBILITY_WINDOW	Default visibility window (kilobases)	float	-1	< 0 disables visibility window
  DEFAULT_FONT_FAMILY	Default font family	string	Arial
  DEFAULT_FONT_SIZE	Default font size	float	10
  SCALE_FONTS	Scale fonts	boolean	FALSE	Scale fonts for high resolution screens. Requires restart.
  BACKGROUND_COLOR	Background color	color	250,250,250
  ENABLE_ANTIALIASING	Enable anti-aliasing	boolean	TRUE
  
  #Tracks
  IGV.chart.track.height	Default numeric track height (pixels)	integer	40
  IGV.track.height	Default feature track height (pixels)	integer	15
  EXPAND_FEATURE_TRACKS	Expand feature tracks	boolean	FALSE
  NORMALIZE_COVERAGE	Normalize coverage data (.tdf files only)	boolean	FALSE
  
  #Variants
  
  ##Variant Colors
  HOMREF.COLOR	Homozygous reference	color	235,235,235
  HETVAR.COLOR	Homozygous variant	color	0,0,255
  HOMVAR.COLOR	Heterozygous variant	color	0,245,255
  NOCALL.COLOR	No call	color	255,255,255
  AF_REF.COLOR	Allele freq - reference	color	0,0,220
  AF_VAR.COLOR	Allel freq - variant	color	255,0,0
  VARIANT_COLOR_BY_ALLELE_FREQ	Color by allele frequency (uncheck to color by allele fraction)	boolean	TRUE
  
  #Mutations
  
  ##Color Options
  COVER_OVERLAY_KEY	Color Mutations	boolean	TRUE
  MUTATION_INDEL_COLOR_KEY	Indel	color	0,200,0
  MUTATION_MISSENSE_COLOR_KEY	Missense	color	170,20,240
  MUTATION_NONSENSE_COLOR_KE	Nonsense	color	50,30,75
  MUTATION_SPLICE_SITE_COLOR_KEY	Splice Site	color	150,0,150
  MUTATION_SYNONYMOUS_COLOR_KEY	Synonymous	color	200,170,200
  MUTATION_TARGETED_REGION_COLOR_KEY	Targeted Region	color	236,155,43
  MUTATION_Truncating_COLOR	Truncating	color	150,0,0
  MUTATION_Non-coding_Transcript_COLOR	Non-coding Transcript	color	0,0,150
  MUTATION_Other_AA_changing_COLOR	Other AA Changing	color	0,150,150
  MUTATION_Other_likely_neutral_COLOR	Other Likely Neutralcolor	225,180,225
  MUTATION_UNKNOWN_COLOR_KEY	Unknown	color	0,180,225
  
  
  #Charts
  CHART.DRAW_TOP_BORDER	Draw top border	boolean	FALSE
  CHART.DRAW_BOTTOM_BORDER	Draw bottom border	boolean	FALSE
  CHART.COLOR_BORDERS	Color borders	boolean	TRUE
  CHART.DRAW_TRACK_NAME	Draw track label	boolean	FALSE
  CHART.DRAW_AXIS	Label Y axis	boolean	FALSE
  CHART.AUTOSCALE	Continuous autoscale	boolean	FALSE
  CHART.SHOW_DATA_RANGE	Show data range	boolean	TRUE
  CN_FREQ.AMP_THRESHOLD	CN freq amplification threshold	float	0.1
  CN_FREQ.DEL_THRESHOLD	CN freq deletion threshold	float	-0.1
  
  #Alignments
  
  ##Track Display Options
  SAM.SHOW_ALIGNMENT_TRACK	Show alignment track	boolean	TRUE
  SAM.SHOW_COV_TRACK	Show coverage track	boolean	TRUE
  SAM.SHOW_JUNCTION_TRACK	Show junction track	boolean	FALSE
  
  ##Downsampling
  SAM.DOWNSAMPLE_READS	Downsample reads	boolean	TRUE
  SAM.SAMPLING_WINDOW	Sampling window size (bases)	integer	50
  SAM.MAX_LEVELS	Number of reads per window	integer	100
  
  ##Alignment Track Options
  
  SAM.MAX_VISIBLE_RANGE	Visibility range threshold (kb)	float	30	Range at which alignments become visibile
  SAM.QUALITY_THRESHOLD	Mapping quality threshold	int	0
  SAM.ALIGNMENT_SCORE_THRESHOLD	Alignment score threshold	int	0
  ---
  SAM.SHADE_BASE_QUALITY	Shade mismatched bases by quality	boolean	TRUE
  SAM.BASE_QUALITY_MIN	Base quality minimum	integer	5
  SAM.BASE_QUALITY_MAX	Base quality maximum	integer	20
  ---
  SAM.SHOW_MISMATCHES	Show mismatched bases	boolean	TRUE
  ---
  SAM.FLAG_LARGE_INDELS	Label indels > label threshold	boolean	TRUE
  SAM.LARGE_INSERTIONS_THRESOLD	Label threshold (bases)	integer	1
  ---
  SAM.HIDE_SMALL_INDEL	Hide indels < show indel threshold	boolean	FALSE
  SAM.SMALL_INDEL_BP_THRESHOLD	Show indel threshold (bases)	integer	0
  ---
  SAM.FLAG_CLIPPING	Flag clipping > flag clipping threshold	boolean	FALSE
  SAM.CLIPPING_THRESHOLD	Flag clipping threshold (bases)	integer	0
  ---
  SAM.QUICK_CONSENSUS_MODE	Quick consensus mode	boolean	FALSE
  SAM.SHOW_INSERTION_MARKERS	Show insertion markers	boolean	FALSE
  ---
  SAM.LINK_READS	Link alignments by tag	boolean	FALSE
  SAM.LINK_TAG	Linking tag	string	READNAME
  ---
  SAM.FILTER_DUPLICATES	Filter duplicate reads	boolean	TRUE
  SAM.FILTER_FAILED_READS	Filter vendor failed reads	boolean	TRUE
  SAM.FILTER_SECONDARY_ALIGNMENTS	Filter secondary alignments	boolean	FALSE
  SAM.FILTER_SUPPLEMENTARY_ALIGNMENTS	Filter supplementary alignments	boolean	FALSE
  SAM.FLAG_UNMAPPED_PAIR	Flag unmapped pairs	boolean	FALSE
  SAM.SHOW_SOFT_CLIPPED	Show soft-clipped bases	boolean	FALSE
  SAM.SHOW_CENTER_LINE	Show center line	boolean	FALSE
  SAM.HIDDEN_TAGS	Hidden SAM tags	string	SA,MD,XA,RG
  ##Coverage Track Options
  SAM.ALLELE_THRESHOLD	Coverage allele-fraction threshold	float	0.2f
  SAM.ALLELE_USE_QUALITY	Quality weight allele fraction	boolean	TRUE
  ##Splice Junction Track
  SAM.SHOW_JUNCTION_FLANKINGREGIONS	Show flanking regions	boolean	FALSE
  SAM.JUNCTION_MIN_FLANKING_WIDTH	Minimum flanking width	integer	0
  SAM.JUNCTION_MIN_COVERAGE	Minimum junction coverage	integer	1
  ##Insert Size Options
  SAM.COMPUTE_ISIZES	Compute insert size thresholds	boolean	TRUE
  SAM.MIN_ISIZE_MIN_PERCENTILE	Minimum (percentile)	float	0.5
  SAM.ISIZE_MAX_PERCENTILE	Maximum (percentile)	float	99.5
  SAM.MIN_INSERT_SIZE_THRESHOLD	Default minimum (bp)	float	50
  SAM.INSERT_SIZE_THRESHOLD	Default maximum (bp)	float	1000
  
  #RNA	RNA
  info Settings below override defaults for RNA alignments.
  
  ##Track Display Options
  SAM.SHOW_ALIGNMENT_TRACK	Show alignment track	boolean	TRUE
  SAM.SHOW_COV_TRACK	Show coverage track	boolean	TRUE
  SAM.SHOW_JUNCTION_TRACK	Show junction track	boolean	TRUE
  
  SAM.MAX_VISIBLE_RANGE	Visibility range threshold (kb)	float	300	Range at which alignments become visibile
  
  ##Splice Junction Track
  SAM.SHOW_JUNCTION_FLANKINGREGIONS	Show flanking regions	boolean	TRUE
  SAM.JUNCTION_MIN_FLANKING_WIDTH	Minimum flanking width	integer	0
  SAM.JUNCTION_MIN_COVERAGE	Minimum junction coverage	integer	1
  
  #Third Gen	THIRD_GEN
  info Settings below override defaults for 3rd-gen (PacBIO, Oxford Nanopore, ...) alignments.
  SAM.MAX_VISIBLE_RANGE	Visibility range threshold (kb)	float	1000	Range at which alignments become visibile
  
  ##Downsampling
  SAM.DOWNSAMPLE_READS	Downsample reads	boolean	FALSE
  
  SAM.FLAG_LARGE_INDELS	Label indels > label threshold	boolean	TRUE
  SAM.LARGE_INSERTIONS_THRESOLD	Label threshold (bases)	integer	1
  ---
  SAM.HIDE_SMALL_INDEL	Hide indels < show indel threshold	boolean	TRUE
  SAM.SMALL_INDEL_BP_THRESHOLD	Show indel threshold (bases)	integer	2
  ---
  SAM.FLAG_CLIPPING	Flag clipping > flag clipping threshold	boolean	FALSE
  SAM.CLIPPING_THRESHOLD	Flag clipping threshold (bases)	integer	0
  ---
  SAM.QUICK_CONSENSUS_MODE	Quick consensus mode	boolean	TRUE
  SAM.SHOW_INSERTION_MARKERS	Show insertion markers	boolean	TRUE
  ---
  SAM.LINK_READS	Link alignments by tag	boolean	FALSE
  SAM.LINK_TAG	Linking tag	string	READNAME
  
  #Cram
  CRAM.CACHE_SEQUENCES	Cache reference sequences	boolean	TRUE
  CRAM.CACHE_SIZE	Cache size (MB)	integer	500
  
  #Proxy
  PROXY.DISABLE_CHECK	Disable check for system proxy	boolean	FALSE
  PROXY.USE	Use proxy	boolean	FALSE
  PROXY.HOST	Proxy host	string	null
  PROXY.PORT	Proxy port	integer	0
  PROXY.WHITELIST	Whitelist	string	null
  PROXY.TYPE	Proxy type	select HTTP|SOCKS|DIRECT	HTTP
  ---
  PROXY.AUTHENTICATE	Authentication required	boolean	FALSE
  PROXY.USERNAME	Username	string	null
  PROXY.PW	Password	string	null
  
  #Advanced
  ---
  PORT_ENABLED	Enable port	boolean	TRUE
  PORT_NUMBER	Port number	integer	60151
  ---
  IGV.genome.sequence.dir	Genome server URL	string	https://s3.amazonaws.com/igv.org.genomes/genomes.txt
  MASTER_RESOURCE_FILE_KEY	Data registry url	string	https://data.broadinstitute.org/igvdata/$$_dataServerRegistry.txt
  ---
  BLAT_URL	Blat url	String	http://genome.cse.ucsc.edu/cgi-bin/hgBlat
  ---
  TOOLTIP.INITIAL_DELAY	Tooltip inital delay (ms)	integer	50
  TOOLTIP.RESHOW_DELAY	Tooltip reshow delay (ms)	integer	50
  TOOLTIP.DISMISS_DELAY	Tooltip dismiss delay (ms)	integer	60000
  ---
  
  #Hidden
  SCORE_VARIANTS	FALSE
  
  SAM.COLOR_BY	UNEXPECTED_PAIR
  SAM.AUTOSORT	FALSE
  SAM.SHADE_CENTER	TRUE
  SAM.SHOW_REF_SEQ	FALSE
  SAM.SHADE_BASE_QUALITY	QUALITY
  SAM.FILTER_ALIGNMENTS	FALSE
  SAM.FILTER_URL	null
  SAM.BISULFITE_CONTEXT	CG
  SAM.FLAG_ZERO_QUALITY	TRUE
  SAM.NOMESEQ_ENABLED	FALSE
  SAM.COUNT_DELETED_BASES_COVERED	FALSE
  SAM.SORT_OPTION	NUCLEOTIDE
  SAM.GROUP_OPTION	NONE
  SAM.COLOR_BY	UNEXPECTED_PAIR
  SAM.SHOW_GROUP_SEPARATOR	TRUE
  SAM.SHOW_ALL_BASES	FALSE
  SAM.SHOW_MISMATCHES	TRUE
  SAM.REDUCED_MEMORY_MODE	FALSE
  SAM.COLOR.A	0,255,0
  SAM.COLOR.C	0,0,255
  SAM.COLOR.G	209,113,5
  SAM.COLOR.N	182,182,182
  SAM.COLOR.T	255,0,0
  
  
  SEARCH_ZOOM	TRUE
  SAVE_GOOGLE_CREDENTIALS	TRUE
  MAX_SEQUENCE_RESOLUTION	2
  DEFAULT_FONT_ATTRIBUTE	0
  TRACK_ATTRIBUTE_NAME_KEY
  OVERLAY_TRACKS_KEY	TRUE
  SHOW_ORPHANED_MUTATIONS	TRUE
  
  OVERLAY_MUTATIONS_WHOLE_GENOME	TRUE
  
  
  PROBE_MAPPING_KEY	FALSE
  PROBE_MAPPING_FILE	null
  USE_PROBE_MAPPING_FILE	FALSE
  CHART.SHOW_ALL_HEATMAP	FALSE
  CHART.COLOR_TRACK_NAME	TRUE
  IGV.track.show.attribute.views	TRUE
  
  BYPASS_FILE_AUTO_DISCOVERY	FALSE
  SHOW_GENOME_SERVER_WARNING	TRUE
  
  OVERLAY_ATTRIBUTE_KEY	LINKING_ID
  DEFAULT_GENOME_KEY	hg19
  IGV.track.height	15
  FLANKING_REGION	2000
  SHOW_SEQUENCE_TRANSLATION	FALSE
  AUTO_UPDATE_GENOMES	TRUE
  GWAS_TRACK_HEIGHT	200
  GWAS_DESCRIPTION_CACHE_SIZE	10000
  GWAS_MIN_POINT_SIZE	3
  GWAS_MAX_POINT_SIZE	7
  GWAS_USE_CHR_COLORS	TRUE
  GWAS_SINGLE_COLOR	FALSE
  GWAS_ALTERNATING_COLORS	FALSE
  GWAS_PRIMARY_COLOR	69,101,183
  GWAS_SECONDARY_COLOR	250,169,10
  GWAS_SHOW_AXIS	TRUE
  ENABLE_ANTIALIASING	TRUE
  NAME_PANEL_WIDTH	160
  GENOME_SPACE_ENABLE	TRUE
  GENOME_SPACE_DM_SERVER	https://dm.genomespace.org/datamanager/v1.0/
  GENOME_SPACE_ATM_SERVER	https://atm.genomespace.org/atm/v1.0/
  GENOME_SPACE_IDENTITY_SERVER	https://identitydev.genomespace.org:8444/identityServer/basic
  DB_ENABLED	FALSE
  DB_HOST
  DB_NAME
  DB_PORT	-1
  CBIO_MUTATION_THRESHOLD	1
  CBIO_AMPLIFICATION_THRESHOLD	0.9
  CBIO_DELETION_THRESHOLD	0.9
  CBIO_EXPRESSION_UP_THRESHOLD	1
  CBIO_EXPRESSION_DOWN_THRESHOLD	1
  DETAILS_BEHAVIOR	HOVER
  SHOW_SIZE_WARNING	TRUE
  SKIP_VERSION
  COLOR.A	0,150,0
  COLOR.C	0,0,255
  COLOR.T	255,0,0
  COLOR.G	209,113,5
  COLOR.N	128,128,128
  
  SASHIMI.SHOW_COVERAGE	TRUE
  SAM.SHOW_DUPLICATES	FALSE
  GENE_LIST_BED_FORMAT	FALSE
  showLOS	TRUE
  DEBUG.PROXY	FALSE
  
  MUTATION_INDEL_COLOR_KEY	Indel	color	0,200,0
  MUTATION_MISSENSE_COLOR_KEY	Missense	color	170,20,240
  MUTATION_NONSENSE_COLOR_KE	Nonsense	color	50,30,75
  MUTATION_SPLICE_SITE_COLOR_KEY	Splice Site	color	150,0,150
  MUTATION_SYNONYMOUS_COLOR_KEY	Synonymous	color	200,170,200
  MUTATION_TARGETED_REGION_COLOR_KEY	Targeted Region	color	236,155,43
  MUTATION_Truncating_COLOR	Truncating	color	150,0,0
  MUTATION_Non-coding_Transcript_COLOR	Non-coding Transcript	color	0,0,150
  MUTATION_Other_AA_changing_COLOR	Other AA Changing	color	0,150,150
  MUTATION_Other_likely_neutral_COLO	Other Likely NeutralR	color	225,180,225
  MUTATION_UNKNOWN_COLOR_KEY	Unknown	color	0,180,225
  