[ProcessRun]
; RunDescription: if specified, a custom description will be used. Will be ignored if a RunId is specified.
;                 otherwise, "Added markers for {MapSet Accession No.} from {Sources}." will be used.
RunDescription="Added repeats for Wm82.a4.v1 from http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Gmax."

[MapSet]
; Either MapSetId or MapSetPath is required.
; MapSetId: id of a target map set.
;MapSetId=12345
; MapSetPath: path of a target map set.
MapSetPath="/Glycine max/Wm82.a4.v1"

[MarkerType]
; To add or update a marker type, specify a type name and description.
;TypeName=Description
;SNP="Single Nucleotide Polymorphism"
REPEAT="Generic marker used to map internal repeats on genome."

[Marker]
; Source (required): a TXT file or GFF file located locally or remotely accessible via URL.
Source=$DATA/soybean/Gmax_508_Wm82.a4.v1.repeatmasked_assembly_v4.0.gff3.gz 
; FileType: {Text (delimited text file)|Gff}
FileType=Gff
; Origin (required): database or institution that the file originate
Origin="Phytozome"
; Coordinate system: 1 (one-based) / 0 (zero-based). Default value is 1.
CoordinateSystem=1
; MappingMethod: method to map markers in the file. e.g. BLAST, RepeatMasker
;                if not specified, 'Unknown' is used.
MappingMethod="RM"
; Tracks (required): comma delimited. Corresponding section(s) named the same must exist
;                    At least one track need to be specified.
Tracks="Wm82.a4.v1_repeat"
; SourceOrganismId: markers are suggested to be unique in a source organism.
;                   Specify a source organism if you want to lookup markers belonging to the organism.
;                   Otherwise, inferred by target MapSet.
;SourceOrganismId=1534
; BypassLookup: When adding new markers, PSH will try to reuse the markers with the same OrganismId and name, assuming they are the same markers
;               mapped onto different positions. To reuse them, a lookup table with existing markers is built.
;               If BypassLookup=true, PSH will skip this step and will issue a database query for each inserted marker in order to 
;               find an identical marker with the same OrganismId and name. When adding just a few markers
;               while the database contains millions of markers with the same OrganismId you can bypass the lookup and 
;               save time and memory. On the contrary, if you insert a large number of markers, leave
;               BypassLookup=false (default), and the lookup will be built from the markers in the database that have
;               the same OrganismId. To reduce the size of the lookup table, use NamePrefixesForLookup (see below).
;BypassLookup=true
; SearchAliases: Indicates if other names besides primary name are searched or not.  Default value is false.
;SearchAliases=false
; Commit frequency: indicates how often the process commits markers. Every N markers.
CommitFrequency=1000

[Wm82.a4.v1_repeat]
; MarkerType (required): type of marker. If new, should be specified in MarkerType section. 
MarkerType="REPEAT"
; TrackName: track name to be displayed on the plate.
TrackName="RepeatMasker"
; TrackDescription: track description shared across maps in the MapSet.
TrackDescription="Repeat regions identified by RepeatMasker."
; TrackType: choose one among 
;            1. GENERIC_BP_TRACK: markers for physical maps.
;            2. MARKER_TRACK: markers for genetic maps.
;            3. HEAT_TRACK: markers for physical maps. Heatmap of physical distance.
;            4. DENSE_BP_MARKER_TRACK: dense marker track for physical maps. Heatmap will not work.
;            5. CYTOBAND_TRACK: cytoband markers. Each marker has to have 'GieStain' qualifier.    
TrackType=DENSE_BP_MARKER_TRACK
; TrackColor: {NamedColor|HTML hex code|R,G,B}
TrackColor=230,248,243
; GeneratedMarkerNamePrefix: in case there are no appropriate values to be used as marker names, generate names for each marker using this prefix.
; For example, if the feature names are not important, they can be named automatically, like TSS1, TSS2... using prefix 'TSS'.
;GeneratedMarkerNamePrefix=TSS

; AddModes: choose a mode to add name, mapping, qualifiers or sequence among
;           1. AddAnyway: Add regardless of duplication. Faster as it does not check.
;           2. AddOrDie: add if not exists; die (throw exception) otherwise.
;           3. AddOrUpdate: add if not exists; update otherwise.
;           4. AddOrSkip: add if not exists; skip otherwise.
MarkerNameAddMode=AddAnyway
MarkerSequenceAddMode=AddAnyway
MarkerQualifierAddMode=AddAnyway
MappingAddMode=AddAnyway
MappingQualifierAddMode=AddAnyway
; GffSource: Gff column 2. Database name or software that generated these features.
;            if not specified, all the sources will be included. 
;GffSource="RepeatMasker"
; GffType: Gff column 3. Feature type. A term from the full Sequence Ontology.
;          if not specified, all the types will be included. 
;GffType="similarity"
; GffMarkerNameAttributeKey (required at least one): Gff attribute key whose value contains marker name.
GffMarkerNameAttributeKey.ID=FULL_NAME
; GffMarkerSequenceAttributeKey: Gff attribute key whose value contains marker sequences.
;GffMarkerSequenceAttributeKey.Seq=SEQ
; GffMarkerQualifierAttributeKey: Gff attribute key whose value contains marker qualifiers.
;GffMarkerQualifierAttributeKey.AttributeKey=qualifierName((:displayText),dataType,dataFormat)
GffMarkerQualifierAttributeKey.Note="Note"
; GffMappingQualifierAttributeKey: Gff attribute key whose value contains mapping qualifiers.
;GffMappingQualifierAttributeKey.AttributeKey=qualifierName((:displayText),dataType,dataFormat)

; ParentGroupName: the new track will be placed under a parent node with this name. 
; To reduce the number of track nodes on the top level, group the tracks of similar type.
;ParentGroupName=marker tracks

; TrackQualifier: Add qualifiers that can help filtering the large track lists when using the Edit tracks interface in webPersephone
;TrackQualifier.Tissue=Liver
;TrackQualifier.Author=JHU

; IsShownFirst: if false, the track will not be shown by default when the map is opened for the first time
IsShownFirst=false
; IsSearchable: If true (default), the track data will be indexed for search. If false, the indexing will be skipped
;IsSearchable=false

[MapMapping]
; LoadListedMapsOnly: if true, only maps listed below will be loaded, otherwise psh will try to match map_names 
; not listed here to MAP_NAME, MAP_ID or ACCESSION_NO. The map will be automatically skipped if no match is found.
;LoadListedMapsOnly=true

; If no mapping is found in this section, it assumes that each MAP_NAME in file exactly matches a MAP_NAME in DB. 
; If map names in file are different from those in DB, map each MAP_NAME in file to its MAP_NAME, MAP_ID or ACCESION_NO in DB.
; Otherwise, marker will be created without mapping.
;MAP_NAME in file=MAP_NAME, MAP_ID or ACCESSION_NO in DB

[DbSequences]
; The ID columns below are used in loading markers.
; If there is no sequence/trigger assigned to these columns, you must specify a sequence for them.
;PROCESS_RUN.RUN_ID=ID_SEQ
;ANALYSIS.ANALYSIS_ID=ID_SEQ
;MARKER_TYPE.MARKER_TYPE_ID=ID_SEQ
;DESCRIPTION.DESCR_ID=ID_SEQ
;TRACK.TRACK_ID=ID_SEQ
;TRACK_STYLE.TRACK_STYLE_ID=ID_SEQ
;MARKER.MARKER_ID=ID_SEQ
;MARKER_NAME.MARKER_NAME_ID=ID_SEQ
;MARKER_NAME_TYPE.MARKER_NAME_TYPE_ID=ID_SEQ
;MARKER_SEQUENCE.MARKER_SEQUENCE_ID=ID_SEQ
;MARKER_SEQUENCE_TYPE.MARKER_SEQUENCE_TYPE_ID=ID_SEQ
;MARKER_QUALIFIER.QUALIFIER_ID=ID_SEQ
;MARKER_QUALIFIER_NAME.QUALIFIER_NAME_ID=ID_SEQ
;QUALIFIER_DISPLAY.QUAL_ID=ID_SEQ
;MK_MAPPING.MAPPING_ID=ID_SEQ
;MAPPING_QUALIFIER.MAPPING_QUALIFIER_ID=ID_SEQ