######################################################################
# SPA PARAMETER FILE
######################################################################

######## GENERAL REMARKS ###############################
# Spa uses a probabilistic Bayesian models to score alignments
# Dynamic programming is used to find the optimal alignment under this model
# To keep running times feasible we use the BLAT gfserver to identify genomic loci
# and only try to align those loci.
# In addition, for each locus, we first find regions of homology between clone and genome
# and only do the dynamic programming for a subset of positions in the dynamic programming matrix
# that are in or near such regions of homology. We call these 'defined positions' of the dynamic
# programming matrix.
# The parameters in this file control
# 1. the specifics of the Bayesian model (i.e. likelihoods of various gene structures and sequencing errors)
# 2. The heuristics that determine defined positions in the dynamic programming matrix (which trade-off running
#    time against alignment accuracy.

######################################################################
# Scoring Parameters

# score_match/score_mismatch - probability per base
# for a mismatch to be introduced by sequencing error
# (or SNP)
# (if both defined, must sum to 1.0; if one defined, other will be
# set to make both to sum to 1.0)
score_match 0.998048223638384
score_mismatch 0.00195177636161648


# score_splice_NNNN - relative probability of various splice juctions
# (first two and last two bases of the intron GT-AG is the canonical boundary)
# (if all are defined, must sum to 1.0; otherwise sum must not exceed
# 1.0, and undefined terms will be set equal to each other so as to
# yield a total sum of 1.0)
score_splice_tttt  0.0001975876
score_splice_tttc  0.0000543107
# score_splice_ttta
# score_splice_tttg
score_splice_ttct  0.0000010345
score_splice_ttcc  0.0003248299
score_splice_ttca  0.0001194836
# score_splice_ttcg
# score_splice_ttat
# score_splice_ttac
score_splice_ttaa  0.0000144829
score_splice_ttag  0.0001324147
# score_splice_ttgt
# score_splice_ttgc
# score_splice_ttga
# score_splice_ttgg
# score_splice_tctt
score_splice_tctc  0.0001246560
# score_splice_tcta
# score_splice_tctg
score_splice_tcct  0.0000987938
score_splice_tccc  0.0008798337
score_splice_tcca  0.0000222415
score_splice_tccg  0.0000206898
score_splice_tcat  0.0000248278
score_splice_tcac  0.0000294830
# score_splice_tcaa
# score_splice_tcag
score_splice_tcgt  0.0000206898
# score_splice_tcgc
# score_splice_tcga
# score_splice_tcgg
# score_splice_tatt
# score_splice_tatc
# score_splice_tata
# score_splice_tatg
# score_splice_tact
# score_splice_tacc
# score_splice_taca
# score_splice_tacg
# score_splice_taat
# score_splice_taac
score_splice_taaa  0.0000413796
# score_splice_taag
# score_splice_tagt
# score_splice_tagc
# score_splice_taga
# score_splice_tagg
# score_splice_tgtt
score_splice_tgtc  0.0003248299
# score_splice_tgta
score_splice_tgtg  0.0000718971
# score_splice_tgct
score_splice_tgcc  0.0019474272
# score_splice_tgca
# score_splice_tgcg
score_splice_tgat  0.0000641384
# score_splice_tgac
score_splice_tgaa  0.0000750005
score_splice_tgag  0.0000615522
score_splice_tggt  0.0000093104
score_splice_tggc  0.0011431113
# score_splice_tgga
score_splice_tggg  0.0000103449
score_splice_cttt  0.0000155174
score_splice_cttc  0.0000377589
# score_splice_ctta
score_splice_cttg  0.0001091387
score_splice_ctct  0.0000268967
score_splice_ctcc  0.0000227588
score_splice_ctca  0.0006020731
# score_splice_ctcg
# score_splice_ctat
score_splice_ctac  0.0002617260
# score_splice_ctaa
score_splice_ctag  0.0001520700
score_splice_ctgt  0.0000450003
score_splice_ctgc  0.0000594832
score_splice_ctga  0.0000574142
score_splice_ctgg  0.0002627605
# score_splice_cctt
# score_splice_cctc
# score_splice_ccta
score_splice_cctg  0.0001029318
score_splice_ccct  0.0001851737
score_splice_cccc  0.0007546604
score_splice_ccca  0.0003739681
# score_splice_cccg
# score_splice_ccat
# score_splice_ccac
# score_splice_ccaa
score_splice_ccag  0.0000579314
# score_splice_ccgt
# score_splice_ccgc
# score_splice_ccga
score_splice_ccgg  0.0000305175
score_splice_catt  0.0000206898
# score_splice_catc
# score_splice_cata
score_splice_catg  0.0001184491
score_splice_cact  0.0001443113
score_splice_cacc  0.0002912089
score_splice_caca  0.0000491383
# score_splice_cacg
score_splice_caat  0.0000103449
# score_splice_caac
# score_splice_caaa
score_splice_caag  0.0001360354
# score_splice_cagt
# score_splice_cagc
# score_splice_caga
score_splice_cagg  0.0000103449
# score_splice_cgtt
# score_splice_cgtc
# score_splice_cgta
# score_splice_cgtg
# score_splice_cgct
# score_splice_cgcc
# score_splice_cgca
# score_splice_cgcg
# score_splice_cgat
# score_splice_cgac
score_splice_cgaa  0.0000103449
# score_splice_cgag
# score_splice_cggt
# score_splice_cggc
# score_splice_cgga
score_splice_cggg  0.0000863799
# score_splice_attt
score_splice_attc  0.0002937952
score_splice_atta  0.0000418968
score_splice_attg  0.0001029318
# score_splice_atct
score_splice_atcc  0.0000222415
# score_splice_atca
# score_splice_atcg
score_splice_atat  0.0001050007
score_splice_atac  0.0015620797
score_splice_ataa  0.0001360354
score_splice_atag  0.0004412100
score_splice_atgt  0.0000310347
# score_splice_atgc
# score_splice_atga
score_splice_atgg  0.0000553452
# score_splice_actt
# score_splice_actc
# score_splice_acta
score_splice_actg  0.0000527590
# score_splice_acct
score_splice_accc  0.0004675894
score_splice_acca  0.0000553452
# score_splice_accg
# score_splice_acat
# score_splice_acac
score_splice_acaa  0.0000056897
score_splice_acag  0.0000625866
# score_splice_acgt
score_splice_acgc  0.0000103449
# score_splice_acga
score_splice_acgg  0.0000196553
score_splice_aatt  0.0000620694
# score_splice_aatc
# score_splice_aata
score_splice_aatg  0.0001577597
score_splice_aact  0.0001081042
score_splice_aacc  0.0000812075
# score_splice_aaca
# score_splice_aacg
score_splice_aaat  0.0000082759
score_splice_aaac  0.0003139677
score_splice_aaaa  0.0008829371
score_splice_aaag  0.0002777606
# score_splice_aagt
score_splice_aagc  0.0000232760
# score_splice_aaga
score_splice_aagg  0.0000662074
score_splice_agtt  0.0000501728
score_splice_agtc  0.0002824158
# score_splice_agta
score_splice_agtg  0.0000450003
# score_splice_agct
score_splice_agcc  0.0023146712
score_splice_agca  0.0004122443
# score_splice_agcg
# score_splice_agat
score_splice_agac  0.0005679349
# score_splice_agaa
# score_splice_agag
# score_splice_aggt
score_splice_aggc  0.0012636294
# score_splice_agga
score_splice_aggg  0.0008560404
score_splice_gttt  0.0000336209
score_splice_gttc  0.0000331037
# score_splice_gtta
score_splice_gttg  0.0004934517
score_splice_gtct  0.0000682763
score_splice_gtcc  0.0000817247
# score_splice_gtca
# score_splice_gtcg
score_splice_gtat  0.0000465521
score_splice_gtac  0.0000460348
score_splice_gtaa  0.0001251733
score_splice_gtag  0.9650963110
# score_splice_gtgt
score_splice_gtgc  0.0000377589
score_splice_gtga  0.0000750005
score_splice_gtgg  0.0005229346
# score_splice_gctt
# score_splice_gctc
# score_splice_gcta
score_splice_gctg  0.0000010345
# score_splice_gcct
score_splice_gccc  0.0002058635
# score_splice_gcca
# score_splice_gccg
# score_splice_gcat
# score_splice_gcac
score_splice_gcaa  0.0000206898
score_splice_gcag  0.0101173112
score_splice_gcgt  0.0000237933
score_splice_gcgc  0.0002079325
# score_splice_gcga
score_splice_gcgg  0.0003279333
score_splice_gatt  0.0000103449
# score_splice_gatc
score_splice_gata  0.0000305175
# score_splice_gatg
# score_splice_gact
score_splice_gacc  0.0001510355
# score_splice_gaca
# score_splice_gacg
score_splice_gaat  0.0000191381
score_splice_gaac  0.0000496555
score_splice_gaaa  0.0000589659
score_splice_gaag  0.0001081042
# score_splice_gagt
score_splice_gagc  0.0000775867
score_splice_gaga  0.0000403451
score_splice_gagg  0.0001215526
score_splice_ggtt  0.0000098277
score_splice_ggtc  0.0000496555
score_splice_ggta  0.0000062069
score_splice_ggtg  0.0000450003
# score_splice_ggct
score_splice_ggcc  0.0001696564
score_splice_ggca  0.0000041380
# score_splice_ggcg
score_splice_ggat  0.0000263795
score_splice_ggac  0.0000817247
# score_splice_ggaa
score_splice_ggag  0.0000817247
score_splice_gggt  0.0001251733
score_splice_gggc  0.0000434486
# score_splice_ggga
score_splice_gggg  0.0000362072


# This parameter defines misorientation
min_diff_misorientation -5.0


# genome non-intron jump scoring curve parameters
# (specified as log(probability))
#These parameters control the probability of sequencing errors leading
#to deletions (from the clone) of various lengths.

score_genome_jump_beta0 -0.000122419302613378
score_genome_jump_beta1 -9.52075314908403
score_genome_jump_beta2 -1.37832181030011
score_genome_jump_beta3 -0.897842026321822
score_genome_jump_alpha -0.195803497949152


# clone non-intron jump scoring curve parameters
# (specified as log(probability))
#These parameters control the probability of sequencing errors leading
#to insertions (into the clone) of various lengths.
score_clone_jump_beta0 -0.000111168806770622
score_clone_jump_beta1 -9.61991347892835
score_clone_jump_beta2 -1.32741032131247
score_clone_jump_beta3 -0.854990206010359
score_clone_jump_alpha -0.2125251949967


# Intron parameters

# score_genome_extension - added to non intron genome jump
# = log of probability to NOT start an intron (controls exon-length distribution)
score_genome_extension -0.00201858766583198


shortest_intron_length 32
longest_intron_length 506084

score_intron -17.7159381759754
score_intron -18.1214032840835
score_intron -15.8063956710909
score_intron -16.0295392224051
score_intron -15.7700280269201
score_intron -15.447254634657
score_intron -15.7144581757653
score_intron -15.5675037628086
score_intron -13.7702041132049
score_intron -12.6345338109909
score_intron -12.3694260605777
score_intron -12.6692924443561
score_intron -12.8717510895168
score_intron -13.1235769482799
score_intron -13.4202238619886
score_intron -13.5481661451985
score_intron -13.7393766494097
score_intron -13.6863936069802
score_intron -13.6114599480385
score_intron -13.7420588146296
score_intron -13.714406913359
score_intron -13.8257518651564
score_intron -14.0105294199102
score_intron -13.9547380602818
score_intron -14.077554885876
score_intron -14.1598182117074
score_intron -14.2164048935924
score_intron -14.1789392531542
score_intron -14.2144953793222
score_intron -14.256709246741
score_intron -14.3009474721809
score_intron -14.3947835019868
score_intron -14.3933369743776
score_intron -14.4715673436338
score_intron -14.5049091488119
score_intron -14.481353057402
score_intron -14.5633634309284
score_intron -14.6628319945606
score_intron -14.7363511635424
score_intron -14.8130368884643
score_intron -14.937319284709
score_intron -15.0343560417925
score_intron -15.0905796907183
score_intron -15.2122872086956
score_intron -15.3421501373134
score_intron -15.4908857160164
score_intron -15.552449779056
score_intron -15.6672939080445
score_intron -15.8191149710294
score_intron -15.9228319051969
score_intron -16.1030747647182
score_intron -16.3022448406674
score_intron -16.4460417215364
score_intron -16.6124537704833
score_intron -16.7588920075363
score_intron -16.9417046278802
score_intron -17.1481368034535
score_intron -17.259096754925
score_intron -17.4404634942939
score_intron -17.5746166922348
score_intron -17.8333721105635
score_intron -17.9520454621306
score_intron -18.1291074824365
score_intron -18.2897560085251
score_intron -18.514305412891
score_intron -18.6581062058291
score_intron -18.8266082778362
score_intron -18.8755003522197
score_intron -19.1697537379708
score_intron -19.4431591240659
score_intron -19.5937762313118
score_intron -19.7258728394749
score_intron -19.7988864424644
score_intron -20.094160683175
score_intron -20.3059649279088
score_intron -20.554842058478
score_intron -20.7700186315049
score_intron -20.9920041602114
score_intron -21.1374282609053
score_intron -21.535134401893
score_intron -21.5414883798948
score_intron -21.8205997051684
score_intron -21.9704421153064
score_intron -22.3240333728744
score_intron -22.5850281924673
score_intron -22.4586317758575
score_intron -23.2018661180692
score_intron -22.9884589874794
score_intron -23.3953037576028
score_intron -23.6074696291609
score_intron -23.9583662125995
score_intron -24.3968393242468
score_intron -24.6983369979533
score_intron -25.052836792381
score_intron -25.9032722160406
score_intron -25.1350031720577
score_intron -25.7781990477874
score_intron -25.9702069460656
score_intron -26.4235864240823
score_intron -26.1635883445992

######################################################################
# end SPA PARAMETER FILE
