#! /usr/bin/perl
#
# Script to make TF binding calls from tables of chip-chip p-values
#
# To regenerate the numbers shown in Figure 2 of the main manuscript
# use this command:
#
# tpm_counts.pl -o counts -t 0.001001 -ids SGD_features.20050416.orfs BLA_YPD_pvalues.tab BLA_MMS_pvalues.tab
#
# To get the genes bound by each TF in either the absence of MMS, 
# presence of MMS, or in both experimental conditions:
#
# tpm_counts.pl -t 0.001001 -ids SGD_features.20050416.orfs BLA_YPD_pvalues.tab BLA_MMS_pvalues.tab
#
#

$t_strict     = 1e-3;
$method       = "TPM";
$output       = "ORFlists";
$comp         = "same";
$IDs_list     = "No_Filter";

$usage =<<USAGE;
usage: $0  [OPTIONS] <pvalue-table-cond1> <pvalue-table-cond2>

  -t <t-strict>      (DEFAULT = $t_strict)
  -m <comp-method>   (DEFAULT = \"$method\")  {\"TPM\"|\"strict\"|\"top\"}
  -c <comparisons>   (DEFAULT = \"$comp\")    {\"all\", \"same\", \"diff\"}
  -ids <file-of-IDs> (DEFAULT = $IDs_list)    {file containing ORF ids used to filter rows}
  -o <output>        (DEFAULT = \"$output\")  {\"counts\"|\"ORFlists\"}

USAGE

die $usage if(@ARGV<2);

while(@ARGV) {
    $arg = shift;
    if($arg eq "-t") { $t_strict = shift; }
    elsif($arg eq "-m") { $method = shift; }
    elsif($arg eq "-c") { $comp = shift; }
    elsif($arg eq "-ids") { $IDs_list = shift; }
    elsif($arg eq "-o") { $output = shift; }
    else { push @argv, $arg; }
}

die $usage if(@argv < 2);

$c1_file = shift(@argv);
$c2_file = shift(@argv);

# precomputed values for the TPM method
@t_stricts = (
2.74878500791020e-45,7.47234101918862e-45,1.99204320218597e-44,5.21090772071724e-44,1.33825077855613e-43,3.37597353934102e-43,8.36984260253371e-43,2.04034404470577e-42,4.89283636123649e-42,
1.15474213228226e-41,2.68327455480597e-41,6.14162000611273e-41,1.38520470943910e-40,3.0798347571154e-40,6.75284265675353e-40,1.460660373426e-39,3.11793802580818e-39,6.57034747682682e-39,1.36726866466779e-38,
2.81061468780234e-38,5.70904392672303e-38,1.14622108120878e-37,2.27530929903753e-37,4.46683192637212e-37,8.67485268459604e-37,1.66701851937784e-36,3.17061481705561e-36,5.97003375775047e-36,1.11312140647458e-35,
2.05560548040118e-35,3.7606635210373e-35,6.81725803542658e-35,1.22480170182482e-34,2.1813239156624e-34,3.85174741027960e-34,6.74467627829653e-34,1.17141312348320e-33,2.01828449912095e-33,3.45027268152291e-33,
5.8532413621142e-33,9.85558885640944e-33,1.64733145489719e-32,2.73375042963097e-32,4.50486220750541e-32,7.37246016838881e-32,1.19843197146113e-31,1.93528276505337e-31,3.10501707096056e-31,4.95027047764261e-31,
7.84322308023024e-31,1.23513595034786e-30,1.93349006121875e-30,3.0090344738081e-30,4.65607684617042e-30,7.16422639310833e-30,1.09628085418004e-29,1.66849033995903e-29,2.525920660464e-29,3.8041140178163e-29,
5.69990647074751e-29,8.49774759948656e-29,1.26067255782288e-28,1.86124106666356e-28,2.73491178469833e-28,4.00001816989667e-28,5.8236493405438e-28,8.44070777586894e-28,1.21800153594041e-27,1.74999266142778e-27,
2.50367141516111e-27,3.56700448647502e-27,5.06112368926969e-27,7.15217661427201e-27,1.00671789678953e-26,1.41151412714753e-26,1.97151222846351e-26,2.74333469595960e-26,3.80321452663959e-26,5.25342536991595e-26,
7.23070154524208e-26,9.91722695313872e-26,1.35549296450400e-25,1.84640165726507e-25,2.50669302002691e-25,3.39192166469218e-25,4.57491776589983e-25,6.15086527087499e-25,8.24378630035361e-25,1.10147970367094e-24,
1.46725889806386e-24,1.94866979749847e-24,2.5804255972904e-24,3.40710820768583e-24,4.48581657164585e-24,5.88948328532954e-24,7.71101739250822e-24,1.0068465943455e-23,1.3111428688259e-23,1.70290104299330e-23,
2.20596556322567e-23,2.85032816548187e-23,3.6736212560561e-23,4.72295172327379e-23,6.05714763564709e-23,7.74950459110634e-23,9.89113539278741e-23,1.25950466706516e-22,1.60010895403129e-22,2.02819589589135e-22,
2.56504487527735e-22,3.23682070953775e-22,4.07562813535346e-22,5.1207792657408e-22,6.4203140380555e-22,8.03282061793286e-22,1.00296107740434e-21,1.24973145506624e-21,1.55409693181186e-21,1.92876906764945e-21,
2.38910269516539e-21,2.953611540858e-21,3.64457770993575e-21,4.48877087797827e-21,5.51829549244989e-21,6.7715870941263e-21,8.29458206708945e-21,1.01420887649855e-20,1.23793920950305e-20,1.50841283299399e-20,
1.83484722281076e-20,2.22816845474836e-20,2.70130748198058e-20,3.26954418984634e-20,3.95090634035906e-20,4.76663148699443e-20,5.74170102751857e-20,6.9054567818031e-20,8.29231184693968e-20,9.9425690090184e-20,
1.19033616966010e-19,1.42297343636456e-19,1.69858813095102e-19,2.02465653024929e-19,2.40987399948794e-19,2.86434030273417e-19,3.39977099466419e-19,4.02973826330213e-19,4.76994498849986e-19,5.63853621746582e-19,
6.65645274037855e-19,7.84783198012005e-19,9.24046199482194e-19,1.08662950349545e-18,1.27620278031616e-18,1.49697563403858e-18,1.75377143118521e-18,2.05211043973977e-18,2.3983033509119e-18,2.79955636724252e-18,
3.2640891621945e-18,3.80126714893815e-18,4.42174964049331e-18,5.13765564064758e-18,5.96274917609611e-18,6.91264626608397e-18,8.00504582755876e-18,9.25998703262208e-18,1.07001358721353e-17,1.2351103935964e-17,
1.42418026979322e-17,1.64048368935228e-17,1.88769409022406e-17,2.16994623959577e-17,2.49188978911626e-17,2.85874852486339e-17,3.27638586004972e-17,3.75137716539008e-17,4.29108958246678e-17,4.90377001954564e-17,
5.59864208734274e-17,6.3860127944503e-17,7.27738988875794e-17,8.28561080249693e-17,9.42498423477196e-17,1.07114454869037e-16,1.21627267528738e-16,1.37985436599622e-16,1.56407994535915e-16,1.77138083257953e-16,
2.00445394989382e-16,2.26628837956898e-16,2.56019445531760e-16,2.88983548740609e-16,3.25926233504724e-16,3.67295105485676e-16,4.13584387025590e-16,4.65339372376713e-16,5.2316126922156e-16,5.87712456396872e-16,
6.59722189756596e-16,7.39992790245675e-16,8.29406350513678e-16,9.2893199877916e-16,1.03963376116904e-15,1.16267906640634e-15,1.29934793951121e-15,1.45104293411940e-15,1.61929985611594e-15,1.80579933453460e-15,
2.01237929909436e-15,2.24104842733626e-15,2.49400062809662e-15,2.77363063201075e-15,3.08255076389393e-15,3.42360897619681e-15,3.79990822729318e-15,4.21482729313121e-15,4.67204310577484e-15,5.17555471758951e-15,
5.72970899528725e-15,6.33922815375672e-15,7.00923924556348e-15,7.74530572823008e-15,8.55346123789698e-15,9.44024570473483e-15,1.04127439525358e-14,1.14786269322603e-14,1.26461957469718e-14,1.39244286335544e-14,
1.53230310748967e-14,1.68524892248398e-14,1.85241268371390e-14,2.03501658989952e-14,2.234379117936e-14,2.451921891225e-14,2.68917698456971e-14,2.94779468977413e-14,3.22955176720520e-14,3.53636020973291e-14,
3.87027654666275e-14,4.23351171651583e-14,4.62844153879428e-14,5.05761781619868e-14,5.52378010013516e-14,6.02986815376866e-14,6.57903514834316e-14,7.1746616300013e-14,7.8203702958979e-14,8.52004162000911e-14,
9.27783037070307e-14,1.00981830638443e-13,1.09858563969716e-13,1.19459367119026e-13,1.29838605349888e-13,1.41054362461693e-13,1.53168669299501e-13,1.66247744634736e-13,1.80362248989332e-13,1.9558755199739e-13,
2.12004013920527e-13,2.29697281955729e-13,2.48758601997841e-13,2.69285146542701e-13,2.91380359441438e-13,3.15154318241562e-13,3.40724114876245e-13,3.68214255489552e-13,3.97757080212457e-13,4.29493203732043e-13,
4.63571977524754e-13,5.00151974653392e-13,5.39401498057301e-13,5.81499113295405e-13,6.26634206732774e-13,6.75007570193101e-13,7.26832013131571e-13,7.82333003415945e-13,8.41749337837023e-13,9.05333843504343e-13,
9.73354111317721e-13,1.04609326274123e-12,1.12385075114269e-12,1.20694319899847e-12,1.29570527230194e-12,1.39049059355175e-12,1.49167269473575e-12,1.59964601176622e-12,1.71482692186263e-12,1.83765482541948e-12,
1.96859327393889e-12,2.10813114565004e-12,2.25678387048147e-12,2.41509470609555e-12,2.58363606674014e-12,2.76301090671686e-12,2.95385416031257e-12,3.15683424008664e-12,3.37265459545428e-12,3.60205533355486e-12,
3.84581490444167e-12,4.10475185268075e-12,4.37972663749481e-12,4.67164352363995e-12,4.98145254525429e-12,5.31015154496887e-12,5.65878829062455e-12,6.02846267199134e-12,6.42032897994057e-12,6.83559827057486e-12,
7.27554081687523e-12,7.74148865048113e-12,8.23483819627442e-12,8.75705300249514e-12,9.30966656917502e-12,9.89428527773048e-12,1.05125914246174e-11,1.11663463620064e-11,1.18573937484985e-11,1.2587662912959e-11,
1.33591723346092e-11,1.41740332425750e-11,1.5034453338152e-11,1.59427406431102e-11,1.69013074774215e-11,1.79126745698542e-11,1.89794753049461e-11,2.0104460109924e-11,2.12905009852064e-11,2.25405961821867e-11,
2.38578750320593e-11,2.52456029295139e-11,2.67071864751888e-11,2.82461787808394e-11,2.98662849412407e-11,3.1571367676909e-11,3.33654531517948e-11,3.525273697016e-11,3.72375903569238e-11,3.9324566525823e-11,
4.15184072397991e-11,4.38240495680934e-11,4.62466328445919e-11,4.87915058320345e-11,5.14642340967624e-11,5.42706075987485e-11,5.72166485017205e-11,6.03086192082493e-11,6.35530306247462e-11,6.6956650661376e-11,
7.05265129719558e-11,7.42699259389813e-11,7.81944819089811e-11,8.23080666834728e-11,8.66188692708493e-11,9.11353919045952e-11,9.58664603333074e-11,1.00821234388028e-10,1.06009218832501e-10,1.11440274502001e-10,
1.17124629736445e-10,1.23072892113589e-10,1.29296060488134e-10,1.35805537342664e-10,1.42613141456376e-10,1.49731120897643e-10,1.57172166346480e-10,1.64949424753097e-10,1.73076513338727e-10,1.81567533945003e-10,
1.90437087738230e-10,1.99700290274916e-10,2.09372786935031e-10,2.1947076872949e-10,2.30010988488407e-10,2.41010777436752e-10,2.52488062164076e-10,2.64461381995029e-10,2.76949906767429e-10,2.89973455024761e-10,
3.03552512629933e-10,3.17708251807258e-10,3.32462550619641e-10,3.47838012887984e-10,3.63857988559926e-10,3.80546594535016e-10,3.97928735953513e-10,4.16030127956026e-10,4.34877317921279e-10,4.54497708189282e-10,
4.74919579277297e-10,4.9617211359597e-10,5.18285419673073e-10,5.41290556892341e-10,5.65219560754913e-10,5.90105468670921e-10,6.15982346288848e-10,6.4288531437025e-10,6.70850576217501e-10,6.99915445662288e-10,
7.30118375622553e-10,7.61498987235632e-10,7.9409809957542e-10,8.2795775996131e-10,8.63121274866825e-10,8.99633241435737e-10,9.37539579613614e-10,9.76887564902725e-10,1.01772586174814e-09,1.06010455756315e-09,
1.10407519740184e-09,1.14969081928682e-09,1.19700599020033e-09,1.24607684274642e-09,1.29696111249251e-09,1.34971817599829e-09,1.40440908954003e-09,1.46109662853840e-09,1.51984532769787e-09,1.58072152186576e-09,
1.64379338761908e-09,1.70913098558733e-09,1.77680630351917e-09,1.84689330010126e-09,1.91946794953737e-09,1.99460828689565e-09,2.07239445423250e-09,2.15290874750092e-09,2.23623566425137e-09,2.32246195213353e-09,
2.41167665820676e-09,2.50397117906742e-09,2.59943931180113e-09,2.69817730576806e-09,2.80028391522916e-09,2.90586045282141e-09,3.01501084389019e-09,3.12784168168647e-09,3.24446228343724e-09,3.36498474729644e-09,
3.48952401018517e-09,3.61819790652821e-09,3.75112722789529e-09,3.88843578355480e-09,4.03025046194753e-09,4.17670129308861e-09,4.32792151190492e-09,4.48404762251617e-09,4.64521946346701e-09,4.81158027391772e-09,
4.98327676080154e-09,5.16045916695555e-09,5.34328134023333e-09,5.53190080360627e-09,5.72647882626111e-09,5.92718049570159e-09,6.13417479086072e-09,6.34763465623167e-09,6.567737077024e-09,6.7946631553529e-09,
7.0285981874682e-09,7.26973174203037e-09,7.51825773944052e-09,7.7743745322315e-09,8.03828498652661e-09,8.31019656457359e-09,8.5903214083595e-09,8.87887642431442e-09,9.17608336910973e-09,9.48216893655807e-09,
9.79736484562149e-09,1.01219079295339e-08,1.04560402260447e-08,1.08000090687894e-08,1.11540671797941e-08,1.15184727631197e-08,1.1893489599651e-08,1.22793871430397e-08,1.26764406168027e-08,1.30849311125862e-08,
1.35051456895984e-08,1.39373774752169e-08,1.43819257667784e-08,1.48390961345539e-08,1.53092005259153e-08,1.57925573707012e-08,1.62894916877830e-08,1.68003351928409e-08,1.73254264073511e-08,1.78651107687931e-08,
1.84197407420775e-08,1.89896759322039e-08,1.95752831981504e-08,2.01769367680001e-08,2.07950183553105e-08,2.14299172767284e-08,2.20820305708561e-08,2.27517631183725e-08,2.34395277634137e-08,2.41457454362167e-08,
2.48708452770308e-08,2.5615264761301e-08,2.63794498261241e-08,2.71638549979875e-08,2.79689435217866e-08,2.87951874911308e-08,2.96430679799378e-08,3.05130751753208e-08,3.14057085117712e-08,3.23214768066407e-08,
3.32608983969252e-08,3.42245012773531e-08,3.52128232397814e-08,3.62264120139026e-08,3.72658254092627e-08,3.83316314585963e-08,3.94244085624781e-08,4.05447456352935e-08,4.16932422525333e-08,4.2870508799409e-08,
4.40771666207967e-08,4.53138481725066e-08,4.65811971738827e-08,4.78798687617322e-08,4.92105296455869e-08,5.05738582642995e-08,5.1970544943973e-08,5.34012920572259e-08,5.48668141837948e-08,5.63678382724724e-08,
5.79051038043881e-08,5.94793629576214e-08,6.10913807731592e-08,6.27419353221916e-08,6.44318178747465e-08,6.61618330696664e-08,6.79327990859222e-08,6.9745547815271e-08,7.16009250362498e-08,7.34997905895119e-08,
7.5443018554502e-08,7.74314974274664e-08,7.94661303008051e-08,8.15478350437599e-08,8.3677544484437e-08,8.58562065931683e-08,8.80847846672008e-08,9.03642575167252e-08,9.26956196522311e-08,9.50798814731947e-08,
9.75180694580949e-08,1.00011226355752e-07,1.02560411377995e-07,1.05166700393653e-07,1.07831186123858e-07,1.10554978338681e-07,1.13339204055069e-07,1.16185007736103e-07,1.19093551491571e-07,1.22066015279839e-07,
1.25103597111036e-07,1.28207513251538e-07,1.31378998429752e-07,1.34619306043199e-07,1.37929708366884e-07,1.41311496762964e-07,1.44765981891698e-07,1.48294493923677e-07,1.51898382753338e-07,1.55579018213754e-07,
1.59337790292687e-07,1.63176109349923e-07,1.67095406335849e-07,1.71097133011312e-07,1.75182762168717e-07,1.79353787854378e-07,1.8361172559212e-07,1.87958112608113e-07,1.92394508056947e-07,1.96922493248943e-07,
2.01543671878675e-07,2.06259670254729e-07,2.11072137530665e-07,2.15982745937199e-07,2.20993191015583e-07,2.26105191852185e-07,2.31320491314263e-07,2.36640856286931e-07,2.42068077911298e-07,2.47603971823790e-07,
2.53250378396641e-07,2.59009162979542e-07,2.64882216142451e-07,2.70871453919559e-07,2.76978818054391e-07,2.83206276246044e-07,2.89555822396573e-07,2.96029476859477e-07,3.02629286689324e-07,3.09357325892471e-07,
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0.399743109121904,0.400014089876459,0.400285156189576,0.400556308045623,0.400827545428969,0.401098868323976,0.401370276715008,0.401641770586424,0.401913349922582,0.402185014707837,
0.402456764926543,0.402728600563050,0.403000521601708,0.403272528026862,0.403544619822857,0.403816796974036,0.404089059464738,0.4043614072793,0.404633840402059,0.404906358817348,
0.405178962509498,0.405451651462839,0.405724425661697,0.405997285090397,0.406270229733261,0.406543259574611,0.406816374598766,0.40708957479004,0.40736286013275,0.407636230611206,
0.407909686209719,0.408183226912598,0.408456852704148,0.408730563568673,0.409004359490475,0.409278240453854,0.409552206443108,0.409826257442532,0.410100393436422,0.410374614409067,
0.410648920344759,0.410923311227785,0.41119778704243,0.411472347772980,0.411746993403715,0.412021723918915,0.412296539302859,0.412571439539823,0.412846424614081,0.413121494509905,
0.413396649211565,0.413671888703329,0.413947212969465,0.414222621994237,0.414498115761907,0.414773694256735,0.415049357462982,0.415325105364904,0.415600937946756,0.415876855192792,
0.416152857087263,0.416428943614419,0.416705114758507,0.416981370503774,0.417257710834464,0.417534135734819,0.41781064518908,0.418087239181485,0.418363917696272,0.418640680717676,
0.41891752822993,0.419194460217267,0.419471476663915,0.419748577554103,0.420025762872059,0.420303032602005,0.420580386728166,0.420857825234763,0.421135348106015,0.421412955326141,
0.421690646879356,0.421968422749874,0.42224628292191,0.422524227379674,0.422802256107375,0.423080369089222,0.423358566309420,0.423636847752174,0.423915213401687,0.42419366324216,
0.424472197257793,0.424750815432785,0.425029517751331,0.425308304197626,0.425587174755864,0.425866129410236,0.426145168144932,0.426424290944141,0.42670349779205,0.426982788672845,
0.427262163570708,0.427541622469823,0.427821165354371,0.428100792208529,0.428380503016478,0.428660297762391,0.428940176430445,0.429220139004812,0.429500185469665,0.429780315809173,
0.430060530007505,0.43034082804883,0.430621209917311,0.430901675597114,0.431182225072402,0.431462858327337,0.431743575346078,0.432024376112783,0.432305260611612,0.432586228826718,
0.432867280742257,0.433148416342381,0.433429635611243,0.433710938532992,0.433992325091777,0.434273795271746,0.434555349057045,0.434836986431818,0.43511870738021,0.435400511886362,
0.435682399934415,0.435964371508508,0.436246426592779,0.436528565171366,0.436810787228404,0.437093092748026,0.437375481714366,0.437657954111556,0.437940509923725,0.438223149135003,
0.438505871729517,0.438788677691394,0.43907156700476,0.439354539653737,0.43963759562245,0.439920734895019,0.440203957455566,0.440487263288207,0.440770652377063,0.44105412470625,
0.441337680259882,0.441621319022075,0.441905040976942,0.442188846108593,0.442472734401140,0.442756705838693,0.443040760405361,0.443324898085249,0.443609118862465,0.443893422721114,
0.444177809645299,0.444462279619123,0.444746832626688,0.445031468652094,0.44531618767944,0.445600989692825,0.445885874676346,0.4461708426141,0.446455893490181,0.446741027288683,
0.4470262439937,0.447311543589322,0.447596926059641,0.447882391388747,0.448167939560728,0.448453570559672,0.448739284369666,0.449025080974794,0.449310960359143,0.449596922506795,
0.449882967401834,0.450169095028339,0.450455305370393,0.450741598412076,0.451027974137465,0.451314432530638,0.451600973575673,0.451887597256644,0.452174303557627,0.452461092462695,
0.452747963955923,0.453034918021381,0.453321954643141,0.453609073805272,0.453896275491845,0.454183559686928,0.454470926374588,0.454758375538891,0.455045907163904,0.455333521233692,
0.455621217732317,0.455908996643844,0.456196857952334,0.456484801641850,0.45677282769645,0.457060936100196,0.457349126837146,0.457637399891358,0.457925755246889,0.458214192887796,
0.458502712798135,0.458791314961959,0.459079999363323,0.45936876598628,0.459657614814883,0.459946545833183,0.460235559025231,0.460524654375078,0.460813831866771,0.461103091484361,
0.461392433211895,0.46168185703342,0.461971362932982,0.462260950894627,0.4625506209024,0.462840372940345,0.463130206992506,0.463420123042925,0.463710121075644,0.464000201074705,
0.464290363024148,0.464580606908014,0.464870932710342,0.465161340415169,0.465451830006536,0.465742401468478,0.466033054785032,0.466323789940236,0.466614606918123,0.466905505702729,
0.467196486278088,0.467487548628233,0.467778692737197,0.468069918589013,0.468361226167713,0.468652615457327,0.468944086441886,0.46923563910542,0.469527273431958,0.46981898940553,
0.470110787010163,0.470402666229884,0.470694627048722,0.470986669450702,0.471278793419851,0.471570998940195,0.471863285995757,0.472155654570562,0.472448104648635,0.472740636213999,
0.473033249250677,0.47332594374269,0.473618719674062,0.473911577028812,0.474204515790963,0.474497535944535,0.474790637473547,0.475083820362018,0.475377084593969,0.475670430153418,
0.475963857024382,0.47625736519088,0.476550954636928,0.476844625346544,0.477138377303743,0.477432210492542,0.477726124896957,0.478020120501002,0.478314197288691,0.478608355244040,
0.478902594351063,0.479196914593773,0.479491315956182,0.479785798422304,0.480080361976151,0.480375006601735,0.480669732283069,0.480964539004163,0.481259426749028,0.481554395501674,
0.481849445246113,0.482144575966354,0.482439787646406,0.48273508027028,0.483030453821983,0.483325908285526,0.483621443644915,0.48391705988416,0.484212756987268,0.484508534938246,
0.484804393721102,0.485100333319844,0.485396353718476,0.485692454901006,0.48598863685144,0.486284899553784,0.486581242992044,0.486877667150224,0.487174172012331,0.487470757562369,
0.487767423784343,0.488064170662256,0.488360998180115,0.488657906321923,0.488954895071682,0.489251964413398,0.489549114331074,0.489846344808713,0.490143655830317,0.490441047379891,
0.490738519441436,0.491036071998956,0.491333705036452,0.491631418537928,0.491929212487384,0.492227086868824,0.492525041666248,0.492823076863658,0.493121192445057,0.493419388394446,
0.493717664695825,0.494016021333196,0.494314458290561,0.494612975551919,0.494911573101273,0.495210250922622,0.495509008999968,0.495807847317311,0.496106765858651,0.496405764607989,
0.496704843549327,0.497004002666663,0.497303241943998,0.497602561365332,0.497901960914666,0.498201440576,0.498501000333333,0.498800640170667,0.499100360072,0.499400160021333,
0.499700040002667,0.5
);

# precomputed values for the TPM method
@t_products = (
2.74878500791020e-47,7.5470644293805e-47,2.03188406622969e-46,5.36723495233876e-46,1.39178080969837e-45,3.54477221630807e-45,8.87203315868573e-45,2.18316812783517e-44,5.28426327013541e-44,
1.25866892418766e-43,2.95160201028657e-43,6.81719820678513e-43,1.55142927457180e-42,3.4802132755404e-42,7.69824062869903e-42,1.6797594294399e-41,3.61680810993749e-41,7.68730654788738e-41,1.61337702430800e-40,
3.34463147848478e-40,6.85085271206764e-40,1.38692750826263e-39,2.77587734482578e-39,5.49420326943771e-39,1.07568173288991e-38,2.0837731492223e-38,3.99497466949007e-38,7.5819428723431e-38,1.42479540028747e-37,
2.65173106971752e-37,4.88886257734849e-37,8.93060802640882e-37,1.61673824640876e-36,2.90116080783099e-36,5.16134152977467e-36,9.10531297570031e-36,1.59312184793715e-35,2.7650497637957e-35,4.76137630050161e-35,
8.13600549333873e-35,1.37978243989732e-34,2.32273735140504e-34,3.88192561007597e-34,6.44195295673274e-34,1.06163426424799e-33,1.73772635861864e-33,2.82551283697792e-33,4.56437509431202e-33,7.32640030691107e-33,
1.16864023895431e-32,1.85270392552179e-32,2.91956999244031e-32,4.57373240018831e-32,7.12379757464074e-32,1.10329086453868e-31,1.69923532397906e-31,2.60284493033608e-31,3.96569543692848e-31,6.01050014814976e-31,
9.06285128848854e-31,1.35963961591785e-30,2.02968281809483e-30,3.01521052799497e-30,4.45790620905829e-30,6.56002979863054e-30,9.60902141189728e-30,1.40115749079424e-29,2.03406256502048e-29,2.93998767119868e-29,
4.23120469162228e-29,6.06390762700754e-29,8.65452150865117e-29,1.23017437765479e-28,1.74162196144588e-28,2.4560345812367e-28,3.45014639981115e-28,4.8282690648889e-28,6.73168971215208e-28,9.3510971584504e-28,
1.29429557659833e-27,1.78510085156497e-27,2.45344226575224e-27,3.36045101622243e-27,4.58724822664924e-27,6.24113586303362e-27,8.46359786691468e-27,1.14406094038275e-26,1.54158803816613e-26,2.07078184290137e-26,
2.77311931734070e-26,3.7024726152471e-26,4.92861289082466e-26,6.5416477587568e-26,8.6576259832765e-26,1.14255975735393e-25,1.50364839153910e-25,1.97341932491718e-25,2.58295145158702e-25,3.37174406512674e-25,
4.38987147081909e-25,5.70065633096374e-25,7.38397872467276e-25,9.54036248101306e-25,1.22960097003636e-24,1.58089893658569e-24,2.02768275552142e-24,2.59457961415422e-24,3.31222553484477e-24,4.21864746345402e-24,
5.36094378932965e-24,6.79732349002928e-24,8.5995753655958e-24,1.08560520433705e-23,1.36752689010582e-23,1.71902361223763e-23,2.15636631641934e-23,2.69941994294308e-23,3.37239034203173e-23,4.2047165674758e-23,
5.23213490241221e-23,6.49794538988759e-23,8.054516738958e-23,9.96507134911176e-23,1.23057989481633e-22,1.51683550908429e-22,1.86628096509513e-22,2.29211206088673e-22,2.81012200557192e-22,3.43918125922629e-22,
4.20180014023664e-22,5.12478744592122e-22,6.24002028337514e-22,7.5853425204435e-22,9.2056117730366e-22,1.11539176795670e-21,1.34929974146686e-21,1.62968780050553e-21,1.96527790772471e-21,2.36633142414638e-21,
2.84490344548765e-21,3.41513624727493e-21,4.09359739559195e-21,4.89966880320328e-21,5.8559938187557e-21,6.98899033867138e-21,8.32943893692726e-21,9.91315612772325e-21,1.17817641215947e-20,1.39835698193152e-20,
1.65745673235426e-20,1.96195799503001e-20,2.31935596070031e-20,2.73830634880852e-20,3.22879303419989e-20,3.80231811045799e-20,4.47211714952229e-20,5.25340272573382e-20,6.16363961184359e-20,7.22285542748569e-20,
8.45399093008375e-20,9.8832945872392e-20,1.15407665616875e-19,1.34606577784967e-19,1.56820303331328e-19,1.82493861424617e-19,2.12133714430307e-19,2.46315655067747e-19,2.85693627786013e-19,3.31009585483835e-19,
3.83104492574376e-19,4.42930596125117e-19,5.11565098450721e-19,5.90225377170048e-19,6.8028591242874e-19,7.83297095812568e-19,9.01006111513672e-19,1.03538009764766e-18,1.18863181434330e-18,1.36324806543369e-18,
1.56202114236863e-18,1.78808358244608e-18,2.04494655874098e-18,2.33654224630413e-18,2.66727053844047e-18,3.04205051828065e-18,3.46637712456904e-18,3.94638348674918e-18,4.48890944318076e-18,5.10157679782905e-18,
5.79287191519313e-18,6.57223630075004e-18,7.45016586497423e-18,8.43831962322578e-18,9.54963864168841e-18,1.07984761012789e-17,1.22007394172549e-17,1.37740454223507e-17,1.55378896958803e-17,1.75138312006268e-17,
1.97256934737222e-17,2.21997837073702e-17,2.49651311504617e-17,2.80537463631307e-17,3.15009029634218e-17,3.53454436187528e-17,3.96301121550918e-17,4.44019137840538e-17,4.97125055827593e-17,5.56186195036656e-17,
6.21825203420157e-17,6.9472501247424e-17,7.75634195338048e-17,8.65372757187353e-17,9.648383890988e-17,1.07501321852580e-16,1.19697109159735e-16,1.33188542462946e-16,1.48103766453063e-16,1.64582640019346e-16,
1.82777716949663e-16,2.02855300920215e-16,2.24996579782588e-16,2.49398844449009e-16,2.76276797984072e-16,3.05863960833409e-16,3.38414178457414e-16,3.74203237991685e-16,4.13530600925979e-16,4.56721259180585e-16,
5.04127722364102e-16,5.56132144419712e-16,6.13148598309303e-16,6.75625507846642e-16,7.44048246272688e-16,8.1894191166915e-16,9.00874289830853e-16,9.90459015764108e-16,1.08835894554815e-15,1.19528975088972e-15,
1.31202374931867e-15,1.43939398361538e-15,1.57829856472885e-15,1.72970529313995e-15,1.89465657434636e-15,2.07427464489642e-15,2.26976712617839e-15,2.48243292398045e-15,2.71366849267657e-15,2.96497448376317e-15,
3.23796279937537e-15,3.53436407234552e-15,3.85603559533704e-15,4.20496972258972e-15,4.58330276885104e-15,4.99332443114392e-15,5.43748776013228e-15,5.91841970899662e-15,6.43893228891916e-15,7.00203436150656e-15,
7.61094409974693e-15,8.26910215040626e-15,8.98018553212204e-15,9.74812230484576e-15,1.05771070477242e-14,1.14716171839929e-14,1.24364301929830e-14,1.34766417509176e-14,1.45976848437972e-14,1.58053498973392e-14,
1.71058059706634e-14,1.85056230621755e-14,2.00117955779259e-14,2.16317670145891e-14,2.33734559111325e-14,2.5245283125222e-14,2.72562004924339e-14,2.94157209284395e-14,3.17339500364558e-14,3.42216192844641e-14,
3.68901208189416e-14,3.97515439841668e-14,4.28187136185364e-14,4.61052302017416e-14,4.96255119291643e-14,5.33948387923873e-14,5.74293987473265e-14,6.17463360541761e-14,6.63638018760839e-14,7.13010072262758e-14,
7.6578278356223e-14,8.22171146803514e-14,8.82402493358256e-14,9.46717124789456e-14,1.01536897422888e-13,1.08862629724644e-13,1.16677239332346e-13,1.25010635907431e-13,1.33894387439535e-13,1.43361802275483e-13,
1.53448014687223e-13,1.6419007410723e-13,1.75627038163542e-13,1.87800069650326e-13,2.00752537573748e-13,2.14530122416743e-13,2.29180925770294e-13,2.44755584482848e-13,2.61307389483581e-13,2.78892409439454e-13,
2.97569619410197e-13,3.17401034669726e-13,3.38451849866879e-13,3.607905837028e-13,3.84489229306928e-13,4.09623410498042e-13,4.36272544121623e-13,4.64520008659466e-13,4.94453319312386e-13,5.26164309761686e-13,
5.59749320820128e-13,5.95309396188151e-13,6.32950485536199e-13,6.7278365513925e-13,7.14925306294929e-13,7.59497401761817e-13,8.06627700460211e-13,8.56450000682763e-13,9.09104392068311e-13,9.6473751659759e-13,
1.02350283887534e-12,1.08556092596910e-12,1.15107973708064e-12,1.22023492333226e-12,1.29321013795572e-12,1.37019735717785e-12,1.45139721210307e-12,1.53701933189898e-12,1.62728269859757e-12,1.72241601383105e-12,
1.82265807782718e-12,1.92825818099611e-12,2.0394765084465e-12,2.15658455777592e-12,2.27986557048658e-12,2.40961497738443e-12,2.54614085832656e-12,2.68976441668792e-12,2.84082046892616e-12,2.99965794962965e-12,
3.16664043244082e-12,3.34214666725416e-12,3.52657113409505e-12,3.72032461409297e-12,3.92383477796948e-12,4.13754679246862e-12,4.36192394516549e-12,4.59744828809407e-12,4.84462130064531e-12,5.10396457219164e-12,
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0.126780529233755,0.126910470656004,0.127040498094319,0.127170611570232,0.127300811105266,0.127431096720937,0.127561468438751,0.127691926280207,0.127822470266794,0.127953100419995,
0.128083816761283,0.128214619312123,0.128345508093971,0.128476483128277,0.128607544436480,0.128738692040012,0.128869925960296,0.129001246218749,0.129132652836775,0.129264145835775,
0.129395725237139,0.129527391062248,0.129659143332476,0.129790982069188,0.129922907293742,0.130054919027485,0.130187017291760,0.130319202107897,0.130451473497221,0.130583831481048,
0.130716276080684,0.130848807317429,0.130981425212573,0.131114129787400,0.131246921063183,0.131379799061187,0.131512763802672,0.131645815308887,0.131778953601072,0.131912178700460,
0.132045490628276,0.132178889405737,0.132312375054051,0.132445947594417,0.132579607048028,0.132713353436065,0.132847186779706,0.132981107100117,0.133115114418456,0.133249208755874,
0.133383390133513,0.133517658572507,0.133652014093982,0.133786456719056,0.133920986468837,0.134055603364427,0.134190307426919,0.134325098677398,0.134459977136939,0.134594942826611,
0.134729995767474,0.134865135980581,0.135000363486974,0.135135678307689,0.135271080463753,0.135406569976186,0.135542146865998,0.135677811154192,0.135813562861762,0.135949402009695,
0.136085328618968,0.136221342710552,0.136357444305408,0.136493633424490,0.136629910088744,0.136766274319106,0.136902726136506,0.137039265561864,0.137175892616093,0.137312607320098,
0.137449409694776,0.137586299761014,0.137723277539692,0.137860343051683,0.137997496317850,0.138134737359049,0.138272066196128,0.138409482849925,0.138546987341273,0.138684579690993,
0.138822259919902,0.138960028048806,0.139097884098503,0.139235828089785,0.139373860043434,0.139511979980223,0.139650187920920,0.139788483886282,0.139926867897060,0.140065339973995,
0.140203900137821,0.140342548409264,0.140481284809041,0.140620109357862,0.140759022076428,0.140898022985432,0.14103711210556,0.141176289457489,0.141315555061887,0.141454908939416,
0.141594351110728,0.141733881596468,0.141873500417274,0.142013207593772,0.142153003146585,0.142292887096324,0.142432859463594,0.142572920268991,0.142713069533104,0.142853307276512,
0.142993633519788,0.143134048283496,0.143274551588191,0.143415143454423,0.14355582390273,0.143696592953645,0.143837450627692,0.143978396945386,0.144119431927235,0.144260555593738,
0.144401767965389,0.14454306906267,0.144684458906057,0.144825937516017,0.144967504913010,0.145109161117489,0.145250906149895,0.145392740030666,0.145534662780227,0.145676674419,
0.145818774967395,0.145960964445817,0.146103242874659,0.146245610274311,0.146388066665151,0.146530612067552,0.146673246501876,0.146815969988479,0.146958782547709,0.147101684199905,
0.147244674965399,0.147387754864515,0.147530923917568,0.147674182144865,0.147817529566708,0.147960966203386,0.148104492075185,0.148248107202379,0.148391811605238,0.148535605304019,
0.148679488318976,0.148823460670353,0.148967522378385,0.149111673463301,0.149255913945321,0.149400243844656,0.149544663181511,0.149689171976084,0.149833770248560,0.149978458019122,
0.150123235307942,0.150268102135184,0.150413058521005,0.150558104485554,0.150703240048972,0.150848465231391,0.150993780052936,0.151139184533725,0.151284678693867,0.151430262553462,
0.151575936132605,0.151721699451381,0.151867552529867,0.152013495388133,0.152159528046241,0.152305650524244,0.152451862842189,0.152598165020113,0.152744557078048,0.152891039036014,
0.153037610914028,0.153184272732094,0.153331024510213,0.153477866268374,0.153624798026561,0.153771819804749,0.153918931622905,0.154066133500988,0.154213425458951,0.154360807516736,
0.154508279694279,0.154655842011509,0.154803494488346,0.154951237144701,0.155099070000479,0.155246993075577,0.155395006389884,0.155543109963281,0.155691303815639,0.155839587966826,
0.155987962436698,0.156136427245105,0.156284982411888,0.156433627956882,0.156582363899913,0.156731190260798,0.156880107059350,0.157029114315369,0.157178212048652,0.157327400278985,
0.157476679026148,0.157626048309912,0.157775508150041,0.15792505856629,0.158074699578408,0.158224431206136,0.158374253469205,0.158524166387341,0.158674169980261,0.158824264267673,
0.158974449269279,0.159124725004774,0.159275091493842,0.159425548756162,0.159576096811404,0.159726735679231,0.159877465379298,0.160028285931252,0.160179197354731,0.160330199669369,
0.160481292894788,0.160632477050605,0.160783752156428,0.160935118231857,0.161086575296486,0.161238123369900,0.161389762471676,0.161541492621383,0.161693313838585,0.161845226142834,
0.161997229553677,0.162149324090654,0.162301509773295,0.162453786621123,0.162606154653655,0.162758613890397,0.162911164350851,0.163063806054510,0.163216539020856,0.163369363269369,
0.163522278819516,0.163675285690761,0.163828383902557,0.16398157347435,0.164134854425579,0.164288226775675,0.164441690544061,0.164595245750153,0.164748892413359,0.164902630553079,
0.165056460188706,0.165210381339625,0.165364394025212,0.165518498264838,0.165672694077864,0.165826981483645,0.165981360501528,0.166135831150851,0.166290393450946,0.166445047421136,
0.166599793080737,0.166754630449059,0.166909559545401,0.167064580389057,0.167219692999312,0.167374897395444,0.167530193596724,0.167685581622414,0.167841061491769,0.167996633224036,
0.168152296838455,0.168308052354259,0.168463899790671,0.168619839166909,0.168775870502182,0.168931993815692,0.169088209126633,0.169244516454191,0.169400915817546,0.169557407235868,
0.169713990728321,0.169870666314063,0.170027434012239,0.170184293841993,0.170341245822458,0.170498289972759,0.170655426312014,0.170812654859334,0.170969975633823,0.171127388654575,
0.171284893940679,0.171442491511215,0.171600181385256,0.171757963581867,0.171915838120107,0.172073805019024,0.172231864297663,0.172390015975057,0.172548260070234,0.172706596602216,
0.172865025590013,0.173023547052630,0.173182161009067,0.173340867478311,0.173499666479346,0.173658558031145,0.173817542152678,0.173976618862903,0.174135788180772,0.174295050125231,
0.174454404715216,0.174613851969658,0.174773391907478,0.174933024547591,0.175092749908905,0.175252568010319,0.175412478870725,0.175572482509008,0.175732578944046,0.175892768194707,
0.176053050279855,0.176213425218344,0.176373893029021,0.176534453730727,0.176695107342293,0.176855853882544,0.177016693370298,0.177177625824365,0.177338651263548,0.17749976970664,
0.17766098117243,0.177822285679698,0.177983683247217,0.178145173893751,0.178306757638059,0.17846843449889,0.178630204494988,0.178792067645088,0.178954023967918,0.179116073482199,
0.179278216206643,0.179440452159957,0.179602781360838,0.179765203827977,0.179927719580059,0.180090328635758,0.180253031013743,0.180415826732676,0.180578715811211,0.180741698267993,
0.180904774121661,0.181067943390848,0.181231206094177,0.181394562250265,0.181558011877721,0.181721554995147,0.181885191621138,0.182048921774281,0.182212745473156,0.182376662736335,
0.182540673582383,0.182704778029858,0.182868976097310,0.183033267803282,0.18319765316631,0.183362132204921,0.183526704937637,0.18369137138297,0.183856131559428,0.184020985485508,
0.184185933179702,0.184350974660495,0.184516109946362,0.184681339055774,0.184846662007192,0.18501207881907,0.185177589509856,0.185343194097991,0.185508892601906,0.185674685040028,
0.185840571430773,0.186006551792553,0.186172626143772,0.186338794502824,0.186505056888099,0.186671413317979,0.186837863810836,0.187004408385039,0.187171047058946,0.187337779850911,
0.187504606779276,0.187671527862382,0.187838543118556,0.188005652566123,0.188172856223398,0.188340154108690,0.1885075462403,0.188675032636521,0.188842613315641,0.189010288295938,
0.189178057595685,0.189345921233146,0.189513879226578,0.189681931594233,0.189850078354353,0.190018319525173,0.190186655124923,0.190355085171823,0.190523609684087,0.190692228679922,
0.190860942177528,0.191029750195096,0.191198652750812,0.191367649862853,0.191536741549389,0.191705927828585,0.191875208718596,0.192044584237571,0.192214054403651,0.192383619234971,
0.192553278749657,0.192723032965831,0.192892881901604,0.193062825575082,0.193232864004363,0.193402997207539,0.193573225202692,0.193743548007901,0.193913965641234,0.194084478120753,
0.194255085464514,0.194425787690565,0.194596584816946,0.19476747686169,0.194938463842825,0.195109545778368,0.195280722686333,0.195451994584724,0.195623361491538,0.195794823424767,
0.195966380402392,0.196138032442391,0.196309779562733,0.196481621781378,0.196653559116283,0.196825591585394,0.196997719206651,0.197169941997989,0.197342259977332,0.197514673162600,
0.197687181571704,0.19785978522255,0.198032484133034,0.198205278321048,0.198378167804473,0.198551152601187,0.198724232729058,0.198897408205949,0.199070679049713,0.199244045278199,
0.199417506909247,0.199591063960691,0.199764716450356,0.199938464396062,0.200112307815621,0.200286246726838,0.20046028114751,0.200634411095429,0.200808636588379,0.200982957644136,
0.201157374280468,0.20133188651514,0.201506494365906,0.201681197850514,0.201855996986706,0.202030891792216,0.20220588228477,0.202380968482089,0.202556150401886,0.202731428061867,
0.202906801479729,0.203082270673166,0.203257835659861,0.203433496457493,0.203609253083732,0.203785105556241,0.203961053892677,0.204137098110689,0.204313238227920,0.204489474262005,
0.204665806230572,0.204842234151243,0.205018758041632,0.205195377919346,0.205372093801985,0.205548905707143,0.205725813652406,0.205902817655353,0.206079917733555,0.206257113904579,
0.206434406185982,0.206611794595316,0.206789279150124,0.206966859867944,0.207144536766305,0.207322309862732,0.207500179174739,0.207678144719837,0.207856206515526,0.208034364579304,
0.208212618928657,0.208390969581067,0.208569416554008,0.208747959864947,0.208926599531346,0.209105335570656,0.209284168000324,0.209463096837791,0.209642122100487,0.209821243805839,
0.210000461971266,0.210179776614178,0.210359187751980,0.210538695402071,0.210718299581840,0.210898000308672,0.211077797599944,0.211257691473024,0.211437681945277,0.211617769034059,
0.211797952756718,0.211978233130596,0.212158610173030,0.212339083901346,0.212519654332868,0.212700321484908,0.212881085374776,0.213061946019771,0.213242903437187,0.213423957644312,
0.213605108658424,0.213786356496798,0.213967701176699,0.214149142715387,0.214330681130114,0.214512316438126,0.214694048656661,0.214875877802951,0.215057803894220,0.215239826947688,
0.215421946980564,0.215604164010053,0.215786478053353,0.215968889127654,0.216151397250139,0.216334002437986,0.216516704708364,0.216699504078436,0.216882400565358,0.217065394186281,
0.217248484958345,0.217431672898688,0.217614958024437,0.217798340352715,0.217981819900637,0.218165396685311,0.218349070723838,0.218532842033313,0.218716710630824,0.218900676533452,
0.219084739758271,0.219268900322348,0.219453158242744,0.219637513536513,0.219821966220701,0.220006516312348,0.220191163828488,0.220375908786147,0.220560751202344,0.220745691094094,
0.220930728478401,0.221115863372264,0.221301095792677,0.221486425756625,0.221671853281087,0.221857378383035,0.222043001079435,0.222228721387244,0.222414539323414,0.222600454904891,
0.222786468148614,0.222972579071512,0.223158787690511,0.223345094022529,0.223531498084477,0.223717999893260,0.223904599465775,0.224091296818913,0.224278091969558,0.224464984934587,
0.224651975730872,0.224839064375276,0.225026250884656,0.225213535275862,0.225400917565740,0.225588397771124,0.225775975908847,0.22596365199573,0.226151426048591,0.226339298084241,
0.226527268119482,0.226715336171111,0.226903502255918,0.227091766390686,0.227280128592191,0.227468588877205,0.227657147262488,0.227845803764799,0.228034558400887,0.228223411187494,
0.228412362141357,0.228601411279206,0.228790558617763,0.228979804173745,0.229169147963862,0.229358590004816,0.229548130313303,0.229737768906014,0.22992750579963,0.230117341010829,
0.230307274556279,0.230497306452643,0.230687436716579,0.230877665364734,0.231067992413753,0.231258417880271,0.231448941780919,0.231639564132318,0.231830284951085,0.232021104253831,
0.232212022057157,0.232403038377661,0.232594153231932,0.232785366636553,0.2329766786081,0.233168089163144,0.233359598318248,0.233551206089968,0.233742912494855,0.233934717549451,
0.234126621270294,0.234318623673913,0.234510724776832,0.234702924595569,0.234895223146633,0.235087620446528,0.235280116511751,0.235472711358793,0.235665405004138,0.235858197464263,
0.236051088755639,0.23624407889473,0.236437167897993,0.236630355781880,0.236823642562835,0.237017028257296,0.237210512881695,0.237404096452455,0.237597778985995,0.237791560498727,
0.237985441007055,0.238179420527379,0.238373499076089,0.238567676669572,0.238761953324206,0.238956329056364,0.239150803882411,0.239345377818706,0.239540050881601,0.239734823087444,
0.239929694452573,0.240124664993323,0.240319734726017,0.240514903666978,0.240710171832518,0.240905539238944,0.241101005902558,0.241296571839651,0.241492237066513,0.241688001599422,
0.241883865454656,0.242079828648479,0.242275891197155,0.242472053116938,0.242668314424076,0.242864675134811,0.243061135265378,0.243257694832007,0.243454353850919,0.243651112338330,
0.243847970310450,0.244044927783481,0.244241984773620,0.244439141297058,0.244636397369976,0.244833753008553,0.245031208228958,0.245228763047356,0.245426417479905,0.245624171542755,
0.245822025252051,0.246019978623932,0.246218031674528,0.246416184419966,0.246614436876364,0.246812789059835,0.247011240986484,0.247209792672411,0.247408444133709,0.247607195386465,
0.247806046446759,0.248004997330665,0.248204048054249,0.248403198633574,0.248602449084693,0.248801799423654,0.2490012496665,0.249200799829265,0.249400449927979,0.249600199978662,
0.249800049997333,0.25
);

$k = scalar @t_stricts;
$p_min = $t_stricts[0];
$p_max = $t_stricts[$k-1];

#############################################
for($i=0.01; $i<=0.5; $i+=0.0001) {
  push @t_liberals, $i;
}
for $i (0..$#t_stricts) {
  push @{ $deviates }, abs($t_strict - $t_stricts[$i]);
}

if( $method eq "TPM" && (($t_strict < $p_min) || ($p_max < $t_strict))) {
  printf STDERR "ERROR: parameter -t out of range, [%f]\n", $t_strict;
  printf STDERR "       please choose a threshold in range [%.3e..%.3e]\n",
         $p_min, $p_max;
  exit();
}

#############################################
## find the minimizer (difference between the 
## desired t_strict and possible values in the table)
##
$dev_ord = &order_of_index( $deviates );
$thr_i = $dev_ord->[0];

$t_strict_fit = $t_stricts[$thr_i];
$t_liberal    = $t_liberals[$thr_i];
$t_product    = $t_products[$thr_i];

printf STDERR ("t_strict_input=%.3e\n", $t_strict);
printf STDERR ("t_strict_fit=%.3e\tt_liberal=%.3e\tt_product=%.3e\n", 
	       $t_strict_fit, $t_liberal, $t_product);

## DEFINE WHICH IDS WILL BE USED
$ID_hash = NULL;
if(-e $IDs_list) {
  $ID_hash = &load_registry($IDs_list);
}

($c1_names, $c1_ids, $c1_desc, $c1_pvals) = &read_pvalues_2($c1_file, $ID_hash);
($c2_names, $c2_ids, $c1_desc, $c2_pvals) = &read_pvalues_2($c2_file, $ID_hash);

$com_names = &get_overlap_set($c1_names, $c2_names);

if($output eq "counts") {
    printf "TF1\tTF2\tC1\tC2\tBoth\n";
    # printf "###\t###\t##\t##\t####\n";
}
$names1 = $c1_names;
$names2 = $c2_names;

if($comp eq "same"){ $names2 = $names1 = $com_names; }

$m1 = scalar @{ $names1 };
$m2 = scalar @{ $names2 };

foreach $tf1 (sort @{ $names1 }) {
    foreach $tf2 (sort @{ $names2 }) {
	next if ( ($comp eq "same") && !($tf1 eq $tf2) );
	next if ( ($comp eq "diff") && ($tf1 eq $tf2 || exists $comps_done{$tf1}{$tf2}) );
	
	$comps_done{$tf1}{$tf2}++;
	$comps_done{$tf2}{$tf1}++;

	if($method eq "TPM") {
	    ($c1_is, $c2_is, $bot_is) = &tpm_bound_in_both($tf1, $tf2, $c1_pvals, $c2_pvals, 
							   $c1_ids, $c2_ids, 
							   $t_liberal, $t_product, $t_strict);
	}
	elsif($method eq "strict") {
	    ($c1_is, $c2_is, $bot_is) = &bernoulli_bound_in_both($tf1, $tf2, $c1_pvals, $c2_pvals, 
								 $c1_ids, $c2_ids, 
								 $t_strict);
	}
	else {
	    ($c1_is, $c2_is, $bot_is) = &top_n_bound_in_both($tf1, $tf2, $c1_pvals, $c2_pvals, 
							     $c1_ids, $c2_ids, 
							     $t_strict);
	}
	
	if($output eq "ORFlists") {
	    @c_ids = @{$c1_ids};
	    printf "%s\t%s\n", $tf1."_".$tf2."_C1_only", join(" ", @c_ids[@{ $c1_is }]);
	    printf "%s\t%s\n", $tf1."_".$tf2."_BOTH",    join(" ", @c_ids[@{ $bot_is }]);
	    printf "%s\t%s\n", $tf1."_".$tf2."_C2_only", join(" ", @c_ids[@{ $c2_is }]);
	}
	else
	{
	    $n1 = $n2 = $n3 = 0;
	    if(@{ $c1_is }) { $n1 = scalar(@{ $c1_is }); }
	    if(@{ $c2_is }) { $n2 = scalar(@{ $c2_is }); }
	    if(@{ $bot_is }){ $n3 = scalar(@{ $bot_is }); }
	    printf "$tf1\t$tf2\t$n1\t$n2\t$n3\n";
	}
    }
}

####################
#
# 1. find the top N genes bound in each condition
# 2. genes appearing in both lists are bound in both conditions
#
sub top_n_bound_in_both {
    my($tf1, $tf2, $ps1, $ps2, $ids1, $ids2, $n) = @_;
    my($i, $i1, $i2, $both, $p1_only, $p2_only);

    my($p1) =  $ps1->{$tf1};
    my($p2) =  $ps2->{$tf2};

    my($ord1) = &order_of_index( $p1 );
    my($ord2) = &order_of_index( $p2 );

    my(%i_reg);
    for($i=0; $i<$n; $i++) {
	$i1 = $ord1->[$i];
	$i2 = $ord2->[$i];
	$i_reg{$i1}++;
	$i_reg{$i2}++;
	#print "$i => $i1 $i2 $ids1->[$i1] $p1->[$i1] $p2->[$i2]\n";
    }
    for($i=0; $i<$n; $i++) {
	$i1 = $ord1->[$i];
	$i2 = $ord2->[$i];
	if($i_reg{$i1} == 2) { push @{ $both }, $i1; }
	else {
	    if($i_reg{$i1} == 1) { push @{ $p1_only }, $i1; }
	    if($i_reg{$i2} == 1) { push @{ $p2_only }, $i2; }
	}
    }
    return($p1_only, $p2_only, $both);
}

####################
# 
# use a strict p-value threshold to find genes bound
#
sub bernoulli_bound_in_both {
    my($tf1, $tf2, $ps1, $ps2, $ids1, $ids2, $p_strict_thr) = @_;

    my($p1) =  $ps1->{$tf1};
    my($p2) =  $ps2->{$tf2};
    my($n) = scalar(@{ $p1 });
    my($i, $both, $p1_only, $p2_only);
    $c = 0;
    for($i=0; $i<$n; $i++) {
        if( ($p1->[$i] <= $p_strict_thr) &&
            ($p2->[$i] >  $p_strict_thr) )
        { push @{ $p1_only }, $i; }

        if( ($p2->[$i] <= $p_strict_thr) &&
            ($p1->[$i] >  $p_strict_thr) )
        { push @{ $p2_only }, $i; }

        if( ($p1->[$i] <= $p_strict_thr) &&
            ($p2->[$i] <= $p_strict_thr) )
        {
            unless($ids1->[$i] eq $ids2->[$i]) {
                print STDERR "ERROR: comparing pvalues from different genes\n";
                printf STDERR "ITER:$i  \"%s\"  \"%s\"\n", $ids1->[$i], $ids2->[$i];
                exit(0);
            }
            push @{ $both }, $i;
        }
    }
    return($p1_only, $p2_only, $both);
}

####################
#
# use the truncated product method to find genes bound
# 
sub tpm_bound_in_both {
    my($tf1, $tf2, $ps1, $ps2, $ids1, $ids2, $p_liberal_thr, $p_square_thr, $p_strict_thr) = @_;

    my($p1) =  $ps1->{$tf1};
    my($p2) =  $ps2->{$tf2};
    my($n) = scalar(@{ $p1 });
    my($i, $both, $p1_only, $p2_only);
    $c = 0;
    for($i=0; $i<$n; $i++) {
        if( ($p1->[$i] <= $p_strict_thr) &&
            ($p2->[$i] > $p_liberal_thr) )
        { push @{ $p1_only }, $i; }

        if( ($p2->[$i] <= $p_strict_thr) &&
            ($p1->[$i] > $p_liberal_thr) )
        { push @{ $p2_only }, $i; }

        if( ($p1->[$i] <= $p_liberal_thr) &&
            ($p2->[$i] <= $p_liberal_thr) &&
            (($p1->[$i] * $p2->[$i]) <= $p_square_thr) )
        {
            unless($ids1->[$i] eq $ids2->[$i]) {
                print STDERR "ERROR: comparing pvalues from different genes\n";
                printf STDERR "ITER:$i  \"%s\"  \"%s\"\n", $ids1->[$i], $ids2->[$i];
                exit(0);
            }
            push @{ $both }, $i;
        }
    }
    return($p1_only, $p2_only, $both);
}


#############################################
## return: a reference to an array that contains a
##         permutation of the indicies of the input array
##         sorted in increasing order
##
## e.g. order_of_index([1,3,2]) returns [0,2,1]
## 
## Like the "order" function in R
##
sub order_of_index {
  my($ref) = shift;
  my($i);

  my(@iar, @iar_sorted, $ret);
  $ret = ();
  #printf "%d\n", $#$ref;
  for $i (0..$#$ref) { @{$iar[$i]} = ($ref->[$i], $i); }
  @iar_sorted = sort { $a->[0] <=> $b->[0] } @iar;
  for $i (0..$#$ref) { $ret->[$i] = $iar_sorted[$i][1]; }
  return $ret;
}

#############################################
##
sub read_pvalues_2 {
    my ($file, $idHash) = @_;
    my ($id, $desc, $i, $p, $ids, $names, $pvals, $descs);
    my(@l);
    my($n_ids) = scalar(keys %{ $idHash });
    open(BLA, $file);
    while(<BLA>){
        chomp;
        @l    = split(/\t/);
        $id   = shift(@l);
        $desc = shift(@l);
        if($. == 1) {
            for $i (0..$#l) {
                push @{ $names }, $l[$i];
            }
        } else {
            if( (exists $idHash->{$id}) || ($n_ids == 0) )
            {
                push @{ $ids }, $id;
                push @{ $descs }, $desc;
                for $i (0..$#l) {
                    $p = $l[$i];
                    ## need to do this to get decreasing sort to work
                    if($p eq "NA") { $p = 1; }
                    push @{ $pvals->{$names->[$i]} }, $p;
                }
            }
        }
    }
    close(BLA);
    #printf STDERR "$file (n,m)=(%d,%d)\n", scalar(@{$ids}), scalar(@{$names});
    return($names, $ids, $descs, $pvals);  ## ref2list, ref2list, ref2list, ref2hash
}

#############################################
##
sub filter_real_number {
    my($r, $alt) = @_;
    if( ($r eq "NA") || ($r eq "Inf") || ($r eq "-Inf") || ($r eq "NaN"))
    { $r = $alt; }
    return($r);
}
#############################################
##
sub get_overlap_set {
    my($rL1, $rL2) = @_;
    my($t, %h1, %h2);
    my($c) = ();

    #printf STDERR "get_overlap_set:: %d %d\n", scalar(@{$rL1}), scalar(@{$rL2});
    foreach $t (@{ $rL1 }) { $h1{$t}++; }
    #printf STDERR "\"%s\"\n",  join("\"\n\"", @{ $rL2 });
    foreach $t (@{ $rL2 }) {
        if(exists $h1{$t}){
            unless(exists $h2{$t}) {
                #push @c, $t;
                push @{ $c }, $t;
                $h2{$t}++;
            }
        }
    }
    #printf STDERR "get_overlap_set:: %d\n", scalar(@c);
    return($c);
}
#############################################
sub load_registry {
    my($file) = shift;
    my($reg);

    open(FILE, $file) or die "can't open $file: $!\n";
    while(<FILE>){
        chomp;
        @l=split;
        $reg->{$l[0]}++;
    }
    close(FILE);

    return($reg);
}