#:gmaj

#----------------------------------------------------------------
# This file specifies input parameters for a Gmaj dataset.
# See below for explanatory comments.
#----------------------------------------------------------------

title = "My favorite genomic region"
datapath = /home/cathy/mydata/favreg/
alignfile = tba.maf mlagan.maf
refseq = any
reconorg = none
tabext = .gff .gtf .bed .ct .trk
nowarn =  maf_version  repeat_type_missing
skipotherseq = false

seq 0:
seqname = human.chr11  hg17.chr11  human
exons   = human.exons.bed  chr11
repeats = human.repeats
links   = human.links
underlays    = human.exons.bed  chr11  exons
#underlays.1 = human-mouse.underlays
#underlays.2 = human-rat.underlays
highlights   = human.highlights
offset = 4730995

seq 1:
seqname = mouse.chr7
exons   = mouse.exons
repeats = mouse.repeats
links   = mouse.links
underlays    = mouse.underlays
#underlays.0 = mouse-human.underlays
#underlays.2 = mouse-rat.underlays
highlights   = mouse.highlights
offset = 0

seq 2:
seqname = rat.chr1
exons   = rat.exons
repeats = rat.repeats
links   = rat.links
underlays    = rat.underlays
#underlays.0 = rat-human.underlays
#underlays.1 = rat-mouse.underlays
highlights   = rat.highlights
offset = 0

#----------------------------------------------------------------
# This file specifies input parameters for Gmaj, including the
# names of all data files.  You can omit this file and just give
# Gmaj the name of your alignment file directly, but then you
# don't get the opportunity to provide annotations, offsets,
# additional alignment files, or other optional features.
#
# Syntax:
#
# Each key=value(s) pair must reside on its own single, separate
# line.  (Note that although the '=' was formerly optional, it
# is now required.)  Other than that, the format is fairly loose.
# Even the order of lines is arbitrary, except that "seq N:"
# defines the current sequence until it is superseded by a new
# "seq N:" line.  Values containing spaces must be enclosed in
# double quotes.  Embedded quotes in such strings can be escaped
# with '\', but there is no way to escape the backslash: quoted
# values should not end with '\' (insert a space before the
# final quote if necessary).  Lines with missing values are
# skipped.  A '#' at the beginning of a line marks a comment
# that will be ignored, except for the identifier tag "#:gmaj"
# at the top, which is mandatory.
#
# Required Fields:
#
# At least one alignfile is required.  You do not have to provide
# a section for every sequence (by default they will still be
# displayed), but for each sequence you do mention, the "seq N:"
# line and the seqname field are also required.  Everything else
# is optional.
#
# File Names and Locations:
#
# Filenames can be relative or absolute (fully qualified paths).
# Gmaj will look for relative names in the following locations:
#
#   1. the separately specified "bundle" file (if any)
#   2. the "datapath" specified here (if any)
#   3. the same directory as this parameters file
#
# If you are using Gmaj's "bundle" feature, you must refer to
# the files located in the bundle by their plain filenames,
# without any path.
#
# Title:
#
# This string will be used as the title for the Gmaj windows.
# Typically it describes the alignment data, including the name
# of the locus.  It does not control the applet button's label,
# however, because the applet has not read this file yet;
# instead there is a separate applet parameter for that.
#
# Reference Sequence:
#
# The refseq field identifies the reference sequence used in the
# alignments.  The default value "any" means that the alignments
# were generated by a sequence-symmetric program such as TBA, so
# the user should be allowed to select the reference sequence
# interactively.  Otherwise, the value must match the appropriate
# sequence name from the MAF files (including the contig name, if
# applicable).
#
# Reconstructed Sequence:
#
# If the alignment files include score rows for an ancestral
# reconstruction, the reconorg field identifies which organism
# these scores apply to.  The default value "none" means Gmaj
# will ignore the scores; otherwise the value must match the
# species prefix of the appropriate sequence names from the MAF
# files.  Contig name extensions (e.g. ".chrX") are omitted, as
# the scores can apply to any contig for that organism.  A score
# can be supplied only once for each base in the ancestral
# genome.
#
# Tabular File Extensions:
# 
# The tabext field specifies which filename extensions should
# be treated as generic, tab-delimited formats (GFF/GTF/BED)
# instead of the old PipMaker-style formats.  The default list
# is ".gff .gtf .bed .ct .trk".  Note that it doesn't actually
# matter which of these is used for a particular file, just
# whether it is in the list.
#
# Warning Suppression:
#
# The nowarn field lists keywords for particular warning
# messages that should not be displayed.  This is especially
# useful for applets, when the administrator has seen the
# warning, checked the data, and determined that everything
# is OK and the end user does not need to see the warning.
# The keyword for each suppressible message is displayed at
# the bottom of the message.
#
# Ignoring Sequences:
#
# The skipotherseq field specifies whether sequences that appear
# in the MAF files but are not mentioned here should be ignored.
# If so, these rows are simply skipped; no adjustments are made
# to remove all-gap columns or join adjacent blocks, and empty
# blocks are kept to preserve the MAF files' block numbering.
# This feature is useful for saving memory, and for reducing the
# number of pips when some species have many aligning contigs.
# The default value is false, so all sequences are displayed.
#
# Sequence Numbers and Sequence Names:
#
# The seqname field serves to match up the parameter entries with
# the sequence name in each row of the MAF alignments (including
# the contig name, if applicable).  The sequence number assigns
# the display order, and is also used to identify the secondary
# sequence for plot-specific underlays (see below).
#
# Multiple values can be given for each seqname keyword; in this
# case the first is the primary name to be used for display, and
# the rest are aliases for it.  This is useful when two MAF files
# use different names for the same sequences, or simply for
# changing the display labels.  Alias resolution is applied to
# MAF seqnames, the refseq field, and the initzoom parameter, but
# not to the reconorg field or annotation files.  All primary and
# alias names must be unique (except in the special case of
# pairwise self-alignments).
#
# Sequence numbers start with 0 and must turn out to be
# consecutive, after Gmaj fills in any gaps you leave with the
# MAF sequences you don't mention here.  Thus by default, if
# the alignment files include ten sequences, the valid sequence
# numbers would be 0-9, and Gmaj will assign any that you omit
# (in the order it encounters them, which is affected by file
# bundling).  However if you set skipotherseq = true, then you
# must assign consecutive numbers because Gmaj will not assign
# any.
#
# File Specification Modifiers:
#
# The generic, tabular annotation formats (GFF/GTF/BED) allow
# entries for several sequences to be combined in one file,
# since they can be distinguished by the "seqname" or "chrom"
# column.  However in this case Gmaj will expect the column
# value to match the seqname from the MAF alignments.  If it
# does not (e.g. if the MAF files include a species prefix but
# the annotation file omits it), you can add a sequence
# designation after the filename to tell Gmaj what to look for
# in the annotation file.
#
# Gmaj has special support for annotation data that represents
# exons or repeats (namely adding exon numbers and inferring
# UTRs, or finding the PipMaker repeat category).  For the exons
# and repeats panels this is automatic, but you can also invoke
# it explicitly for files used as linkbars, underlays, or text
# highlights by adding a type hint of "exons" or "repeats" after
# the filename.  This only works if the file is in a generic
# (GFF/GTF/BED) format and contains the appropriate type of data
# (genes/exons or repeats).
#
# Underlays and Highlights:
#
# Gmaj allows you to specify color underlays independently for
# each plot, i.e. for each combination of reference and
# secondary sequences.  Thus in the "seq 1:" section, the
# "underlays.0" entry specifies the underlay file to be used
# when sequence 1 is the reference and sequence 0 is the second
# sequence.  Note that there is e.g. no "underlays.1" entry in
# the "seq 1:" section, since we do not usually have plots
# aligning sequences with themselves.
#
# However, specifying a quadratic number of files quickly becomes
# burdensome as the number of sequences grows.  For the common
# case where the same underlay file is used for most or all of a
# particular reference sequence's plots, the plain "underlays"
# entry (without a number) provides a default for that reference
# sequence.  This can still be overridden as needed by numbered
# entries for special plots.
#
# The highlights file specifies colors for a particular row of
# the text display, so there is only one for each sequence.  If
# you omit it, Gmaj will build default highlights based on the
# exons file (if you provided one).
#
# Offsets:
#
# The offset parameter is used for display purposes only.  It
# specifies an adjustment to be added to all position labels and
# displayed references for a particular sequence.  For example,
# this allows positions to be labeled with respect to some larger
# region.  However, note that all annotations must still be
# specified relative to the sequences referred to in the MAF
# files.
#
#----------------------------------------------------------------
# Cathy Riemer, June 2008