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# SPA TOP PARAMETER FILE
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# tilesize (used to create genomic locus index)
#		values outside the range [1,15] yield error
tilesize 16 

# tileoverlay (the number of tiles which overlap at each position)
#		values outside the range [1,tilesize] yield error
tileoverlay 2 

# locus_expand (the number of positions to expand the locus beyond
#		the alignments found by blat)
maximum_locus_expand 50000 
locus_expand 2000 

# clone_expand (the number positions to expand the clone when retiling 
#               is necessary)
clone_expand 70

# best_locus_list_size_max (max number of blat alignments to align
#		through spa and compare)
best_locus_list_size_max 100

######################################################################
# Diagonal Extension Parameters
                                                                                                                       
define_radius 4
# This parameter controls how much 'fuzz' is added to the end of diagonals in the dynamic programming matrix
# Larger numbers mean longer running time and more accurate alignments.
                                                                                                                       
######################################################################
# Control the the starting tile size
# if number of cells > init_cell_number_cutoff
# the tile size will be increased to keep the number of cell
# less than this cutoff
init_cell_number_cutoff 120000
#total number of positions in the dynamic programming matrix that are allowed.
#Larger number mean longer running time and more accurate alignments
                                                                                                                       
                                                                                                                       
# Control the number of cells occuring from an extension of the locus
extension_cell_number_cutoff 50000
#number of extra positions in the dynamic programming matrix that are allowed when doing extensions.
#Larger numbers mean longer running time and more accurate alignments
                                                                                                                       
# Control the number of cells occuring during retiling
inside_retiling_cell_number_cutoff 25000
#Number of extra positions in the dynamic programming matrix that are allowed at each retiling step.


######################################################################
# Dynamic Retiling Parameters
                                                                                                                       
# retile_genomic_gap_lower_limit (any genomic gaps shorter than this
#               will not be retiled in an effort to align them)
#gaps this small should have been covered by the 'fuzz' at the end of diagonals
retile_genomic_gap_lower_limit 3
                                                                                                                       
# retile_genomic_gap_upper_limit (any genomic gaps longer than this
#               will not be retiled in an effort to align them)
retile_genomic_gap_upper_limit 200000
                                                                                                                       
# retile_poly_a_percentage (the percentage of A (or T in complement)
#               bases in unaligned 5' tail (or 3' tail) to disqualify
#               tail from consideration with dynamic tile resizing)
#If the tail of the clone fails to map and contains more than this percentage of As
#we will assume that it is a poly-A tail that was not removed
retile_poly_a_percentage 75
                                                                                                                       
# retile_tilesize (finegrain tilesize to resolve genome gaps)
#               values outside of the range [1,15] yield error
#this is now superseded by a recursive lowering of tilesize in retiling
retile_tilesize 8
                                                                                                                       
# retile_tileoverlay (tileoverlay used to resolve genome gaps)
#               values outside of [1,retile_tilesize] yield error
#how many overlapping tiles per sequence segment
#(2 means that a tile of size l is shifted by l/2)
retile_tileoverlay 2

# retile_exon_extension (when constructing exons for the retiling,
#               an exon will include all aligned genome positions
#               which are adjacent to another aligned genome position
#               in the exon, and where the difference in offset in
#               either clone offset or genome offset is no more than
#               this value + 1 (i.e. 0 means each offset must be
#               exactly adjacent to the adjacent aligned position)
#When deciding what region to retile we first construct a set of exons
#we consider neighboring aligned areas separated by less than retile_exon_extension
#bases as part of the same exon.
retile_exon_extension 3

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# end SPA TOP PARAMETER FILE
