PSIsigma-ir-v.1.2.pl

=begin
PSI-Sigma: A splicing-detection method for short-read and long-read RNA-seq data
© Kuan-Ting Lin, 2018-2024
PSI-Sigma is free for non-commercial purposes by individuals at an academic or non-profit institution.
For commercial purposes, please contact tech transfer office of CSHL via narayan@cshl.edu
=end
=cut
#!/usr/bin/perl -w

eval unpack u=>q{_=7-E('-T<FEC=#L*(R`)=7-E(%-T871I<W1I8W,Z.D)A<VEC('%W*#IA;&PI.PH)"B`@("!M>2`H)&1B+"1B_86TL)'1Y<&4I(#T@0$%21U8["B`@("`*("`@("1B86T]?G,O*"XJ*5PO+R\["B`@("`*("`@(&UY("5T;7`[_"B`@("!M>2`E=6YI<75E.PH@("`@;7D@*"1G8VAR+"1S=&%R="PD96YD*2`]("@B+2(L,"PP*3L*("`@(&UY_("1E>&]N<SL*("`@(&UY("1M87@@/2`P.PH@("`@;7D@)6)E9#L*("`@(`H@("`@;7D@)'-T87)T=&EM92`]_('1I;64["@H@("`@;7D@)6)I;CL*("`@(&UY("1B:6YS:7IE(#T@,3`P.PH@("`@;7D@0&-H<F]M;W-O;65S_.PH@("`@;7D@)')E861F;W)M870@/2`B<VEN9VQE+65N9"(["B`@("`*("`@('!R:6YT(")0<F]C97-S:6YG_("1B86TN+BY<;B(["B`@("!O<&5N*$E.4%54+"`B+7PB+")S86UT;V]L<R!I9'AS=&%T<R`B("X@)&)A;2D@_;W(@9&EE("0A.PH)=VAI;&4@*&UY("1I;G!U="`](#Q)3E!55#XI('L*"0EC:&]M<"`D:6YP=70["@D);7D@_*"1C:'(L)&QE;F=T:"PD;G5M+"1Z97)O*2`]('-P;&ET*"]<="\L)&EN<'5T*3L*"0EN97AT(&EF*"1C:'(]_?B];7"I<+ETO*3L*"0EP=7-H*$!C:')O;6]S;VUE<RPD8VAR*3L*"7T*"6-L;W-E*$E.4%54*3L*"0H);W!E_;BA)3E!55"P@(BU\(BPB<V%M=&]O;',@=FEE=R`M9B`R("(@+B`D8F%M("X@(B!\(&AE860@+6X@-2(I(&]R_(&1I92`D(3L*"7=H:6QE("AM>2`D:6YP=70@/2`\24Y0550^*2!["@D)8VAO;7`@)&EN<'5T.PH)"21R96%D_9F]R;6%T(#T@(G!A:7)E9"UE;F0B.PH)?0H)8VQO<V4H24Y0550I.PH)<')I;G0@(G)E860@9F]R;6%T(#T@_(B`N("1R96%D9F]R;6%T("X@(EQN(CL*"6EF*"1R96%D9F]R;6%T(&5Q(")S:6YG;&4M96YD(B`F)B`D='EP_92`]/2`Q*7L*"0EP<FEN="`B6U=A<FYN:6YG73H@5&AE('5S92!O9B!S:6YG;&4M96YD('-H;W)T(')E861S_(&ES(&YO="!R96-O;6UE;F1E9"!F;W(@86QT97)N871I=F4@<W!L:6-I;F<@86YA;'ES:7,N7&XB.R`*"7T*_"0H)<WES=&5M*")M:V1I<B!<7W=O<V]S871M<"(I.PH*9F]R96%C:"!M>2`D:6-H<BA`8VAR;VUO<V]M97,I_>PH);7D@)6%N;F\["B`@("!M>2`E:6YT<F]N<SL*("`@("-M>2`D8V]U;G1I<B`](#`["B`@("!O<&5N*$9)_3$4L(B1D8B(I('Q\(&1I92`B06)O<G1I;F<N+B!#86XG="!O<&5N("1D8B`Z("0A7&XB.PH@("`@=VAI;&4H_;7D@)&QI;F4]/$9)3$4^*7L*("`@("`@("!C:&]M<"`D;&EN93L*("`@("`@("!N97AT(&EF*"1L:6YE/7XO_7EPC+RD["B`@("`@("`@;F5X="!I9B@D;&EN92!E<2`B(BD["@D);7D@*"1C:'(L)&DQ<RPD:3%E+"1I,G,L_)&DR92PD=&5S+"1T964L)&%N;F\L)&%S+"1A92PD;F%M92PD9VXI(#T@<W!L:70H+UQT+RPD;&EN92D["@H)_"6YE>'0@:68H)&-H<B!N92`D:6-H<BD["B`@("`@("`@;F5X="!I9B@D;F%M92%^+UQ?4EQ?+RD["@D);7D@_)&,Q(#T@)&%S("L@,3L*"0EM>2`D8S(@/2`D864@+2`Q.PH)"6UY("1I;G1E<G9A;"`]('-P<FEN=&8H(B5D_(BPH)&%E+21A<RDO-2D["@D);7D@)&,S(#T@*"1A<RLD:6YT97)V86PM,2D["@D);7D@)&,T(#T@*"1A<RLH_)&EN=&5R=F%L*C(I+3$I.PH)"6UY("1C-2`]("@D87,K*"1I;G1E<G9A;"HS*2TQ*3L*"0EM>2`D;&]C(#T@_(B1I,G-<="1I,F4B.PH@("`@("`@("1A;FYO>R1C:')]>R1C,7U[)&QO8WTK*SL*("`@("`@("`D86YN;WLD_8VAR?7LD8S)]>R1L;V-]*RL["B`@("`@("`@)&%N;F][)&-H<GU[)&,S?7LD;&]C?2LK.PH@("`@("`@("1A_;FYO>R1C:')]>R1C-'U[)&QO8WTK*SL*("`@("`@("`D86YN;WLD8VAR?7LD8S5]>R1L;V-]*RL[("`@"B`@_("`@("`@)&EN=')O;G-[)&-H<GU[)&QO8WU[)&,Q?2`](#`["B`@("`@("`@)&EN=')O;G-[)&-H<GU[)&QO_8WU[)&,R?2`](#`["B`@("`@("`@)&EN=')O;G-[)&-H<GU[)&QO8WU[)&,S?2`](#`["B`@("`@("`@)&EN_=')O;G-[)&-H<GU[)&QO8WU[)&,T?2`](#`["B`@("`@("`@)&EN=')O;G-[)&-H<GU[)&QO8WU[)&,U?2`]_(#`["B`@("`@("`@(R1C;W5N=&ER*RL["B`@("`@("`@(VQA<W0@:68H)&-O=6YT:7(@/3T@-2D["B`@("!]_"B`@("!C;&]S92A&24Q%*3L*"@EM>2`D8V]U;G0@/2`P.PH);7D@)&%D9"`]("(B.PH)(R-&;W(@26QL=6UI_;F$@<VAO<G0@<F5A9',*"6EF*"1T>7!E(#T](#$I>PH)"21A9&0@/2`B+48@,C4V("UF(#(@+7$@,C4U(B!I_9B@D<F5A9&9O<FUA="!E<2`B<&%I<F5D+65N9"(I.PH)"21A9&0@/2`B+48@,C4V("UQ(#(U-2(@:68H)')E_861F;W)M870@97$@(G-I;F=L92UE;F0B*3L*"7T*"@EP<FEN="`B1&]I;F<N+BX@)&EC:')<;B(["@EO<&5N_*$E.4%54+"`G+7PG+")S86UT;V]L<R!V:65W("(@+B`D861D("X@(B`B("X@)&)A;2`N("(@(B`N("1I8VAR_("X@(B(I(&]R(&1I92`D(2`N(")<<B(@+B`B*&5R<F]R*21A9&0@)&)A;2`D:6-H<EQR(CL*"7=H:6QE("AM_>2`D:6YP=70@/2`\24Y0550^*2!["@D)8VAO;7`@)&EN<'5T.PH)"6YE>'0@:68H)&EN<'5T(&5Q("(B*3L*_"0DD8V]U;G0K*SL*"0EM>2!`87)R87D@/2!S<&QI="@O7'0O+"1I;G!U="D["@D);7D@*"1N86UE+"1C:'(L_)&9L86<L)'-S+"1C:6=A<BD@/2`H)&%R<F%Y6S!=+"1A<G)A>5LR72PD87)R87E;,5TL)&%R<F%Y6S-=+"1A_<G)A>5LU72D["@D):68H(21C:6=A<BE["@D)"7!R:6YT(")P<F]B;&5M871I8R!I;G!U="`]("1I;G!U=%QN_(CL*"0D);F5X=#L*"0E]"@D)(R-&;W(@26QL=6UI;F$@<VAO<G0@<F5A9',*"0EI9B@D='EP92`]/2`Q*7L*_"0D);F5X="!I9B@D8VEG87(]?B];3E-(*ETO*3L*"0E]"@D)(R-&;W(@36EN24].(&QO;F<@<F5A9',*"0EI_9B@D='EP92`]/2`R*7L*"0D);F5X="!I9B@D8VEG87(@97$@(BHB*3L*"0E]"@H)"6UY($!#(#T@<W!L:70H_+UM!+5I=+RPD8VEG87(I.PH)"6UY($!,(#T@<W!L:70H+ULP+3E=*B\L)&-I9V%R*3L*"0EM>2`D;F,@/2!S_8V%L87(@0$,["@D);7D@)&YL(#T@<V-A;&%R($!,.PH)"0H)"6EF*"1T>7!E(#T](#$I>PH)"0EF;W(H;7D@_)&D],#LD:3PD;F,[)&DK*RE["@D)"0EI9B@A)$Q;)&DK,5TI>PH)"0D)"7!R:6YT(")I(#T@)&E<;B(["@D)_"0D)<')I;G0@(F,@/2`D;F-<;B(["@D)"0D)<')I;G0@(FP@/2`D;FQ<;B(["@D)"0D)<')I;G0@(D-;)&E=_(#T@(B`N("1#6R1I72`N(")<;B(["@D)"0D)<')I;G0@(DQ;)&E=(#T@(B`N("1,6R1I72`N(")<;B(["@D)_"0D)<')I;G0@(F-I9V%R(#T@)&-I9V%R7&XB.PH)"0D)"65X:70["@D)"0E]"@D)"0EI9B@D3%LD:2LQ72!N_92`B32(I>PH)"0D)"21S<RL])$-;)&E=(&EF*"1,6R1I*S%=(&5Q(").(B!\?"`D3%LD:2LQ72!E<2`B1"(I_.PH)"0D)?65L<V5["@D)"0D);7D@)&YB(#T@)$-;)&E=.PH)"0D)"69O<BAM>2`D:CTP.R1J/"1N8CLD:BLK_*7L*"0D)"0D);7D@)'!O<R`]("1S<RLD:CL*"0D)"0D):68H<V-A;&%R(&ME>7,@)7LD86YN;WLD8VAR?7LD_<&]S?7T@/3T@,"E["@D)"0D)"0EN97AT.PH)"0D)"0E]96QS97L*"0D)"0D)"69O<F5A8V@@;7D@)&QO8RAK_97ES("5[("1A;FYO>R1C:')]>R1P;W-]('TI>PH)"0D)"0D)"6YE>'0@:68H(21A;FYO>R1C:')]>R1P;W-]_>R1L;V-]*3L*"0D)"0D)"0DD:6YT<F]N<WLD8VAR?7LD;&]C?7LD<&]S?2LK.PH)"0D)"0D)?0H)"0D)"0E]_"@D)"0D)?0H)"0D)"21S<RL])$-;)&E=.PH)"0D)?0H)"0E]"@D)?0H)"6EF*"1T>7!E(#T](#(I>PH)"0EM_>2`D;&]N9TX@/2`P.PH)"0EF;W(H;7D@)&D],#LD:3PD;F,[)&DK*RE["@D)"0EI9B@D3%LD:2LQ72!E<2`B_3B(I>PH)"0D)"6EF*"1#6R1I72`^(#4P*7L*"0D)"0D))&QO;F=.(#T@,3L*"0D)"0D);&%S=#L*"0D)"0E]_"@D)"0E]"@D)"7T*"0D);F5X="!I9B@D;&]N9TX@/3T@,2D["@D)"69O<BAM>2`D:3TP.R1I/"1N8SLD:2LK_*7L*"0D)"6EF*"$D3%LD:2LQ72E["@D)"0D)<')I;G0@(FD@/2`D:5QN(CL*"0D)"0EP<FEN="`B8R`]("1N_8UQN(CL*"0D)"0EP<FEN="`B;"`]("1N;%QN(CL*"0D)"0EP<FEN="`B0ULD:5T@/2`B("X@)$-;)&E=("X@_(EQN(CL*"0D)"0EP<FEN="`B3%LD:5T@/2`B("X@)$Q;)&E=("X@(EQN(CL*"0D)"0EP<FEN="`B8VEG87(@_/2`D8VEG87)<;B(["@D)"0D)97AI=#L*"0D)"7T*"0D)"6EF*"1,6R1I*S%=(&5Q(").(B!\?"`D3%LD:2LQ_72!E<2`B22(@?'P@)$Q;)&DK,5T@97$@(E,B*7L*"0D)"0DD<W,K/21#6R1I72!I9B@D3%LD:2LQ72!E<2`B_3B(I.PH)"0D)?65L<V5["@D)"0D);7D@)&YB(#T@)$-;)&E=.PH)"0D)"69O<BAM>2`D:CTP.R1J/"1N8CLD_:BLK*7L*"0D)"0D);7D@)'!O<R`]("1S<RLD:CL*"0D)"0D):68H<V-A;&%R(&ME>7,@)7LD86YN;WLD8VAR_?7LD<&]S?7T@/3T@,"E["@D)"0D)"0EN97AT.PH)"0D)"0E]96QS97L*"0D)"0D)"69O<F5A8V@@;7D@)&QO_8RAK97ES("5[("1A;FYO>R1C:')]>R1P;W-]('TI>PH)"0D)"0D)"6YE>'0@:68H(21A;FYO>R1C:')]>R1P_;W-]>R1L;V-]*3L*"0D)"0D)"0DD:6YT<F]N<WLD8VAR?7LD;&]C?7LD<&]S?2LK.PH)"0D)"0D)?0H)"0D)_"0E]"@D)"0D)?0H)"0D)"21S<RL])$-;)&E=.PH)"0D)?0H)"0E]"@D)?0H)?0H)8VQO<V4H24Y0550I.PH*_("`@('!R:6YT(")/=71P=70N+BX@)&EC:')<;B(["@EO<&5N*$]55"PB/E]W;W-O<V%T;7`O(B`N("1B86T@_+B`B+B(@+B`D:6-H<B`N("(N25)T;7`N='AT(BD@?'P@9&EE(")!8F]R=&EN9RXN($-A;B=T(&]P96X@;W5T_<'5T=&UP9FEL92YT>'0@.B`D(5QN(CL*"69O<F5A8V@@;7D@)&-H<BAS;W)T(&ME>7,@)6EN=')O;G,I>PH)_"69O<F5A8V@@;7D@)&QO8RAS;W)T(&ME>7,@)7L@)&EN=')O;G-[)&-H<GT@?2E["@D)"6UY("@D<W,L)&5E_*2`]('-P;&ET*"]<="\L)&QO8RD["@D)"6UY($!V86QU97,["@D)"6UY("1P87-S(#T@,#L*"0D)9F]R96%C_:"!M>2`D<&]S*'-O<G0@:V5Y<R`E>R`D:6YT<F]N<WLD8VAR?7LD;&]C?2!]*7L*"0D)"6UY("1V(#T@,#L*_"0D)"6EF*"$D:6YT<F]N<WLD8VAR?7LD;&]C?7LD<&]S?2E["@D)"0D))'8@/2`P.PH)"0D)?65L<V5["@D)_"0D))'8@/2`D:6YT<F]N<WLD8VAR?7LD;&]C?7LD<&]S?3L*"0D)"0DD<&%S<RLK.PH)"0D)?0D*"0D)"7!U_<V@H0'9A;'5E<RPD=BD["@D)"7T*"0D)(VYE>'0@:68H)'!A<W,@/"`S('Q\('-C86QA<B!`=F%L=65S(#T]_(#`I.PH)"0EM>2`D=VET:&EN;F]R;6%L(#T@,#L*"0D);7D@)&%V9R`](&%V97)A9V4H0'9A;'5E<RD["@D)_"6UY("1S=&1E=B`]('-T9&5V*"1A=F<L0'9A;'5E<RD["@D)"6UY("1N=6T@/2!S8V%L87(@0'9A;'5E<SL*_"0D);7D@)&UE9&EA;B`]('-P<FEN=&8H(B5D(BQM961I86XH0'9A;'5E<RDI.PH)"0EM>2`D;6%R9VEN;V9E_<G)O<B`]("1S=&1E=B`O('-Q<G0H)&YU;2D["@D)"6UY("1Z(#T@,2XY-CL*"0D);7D@)&YO<FUA;')A=&EO_(#T@,"XV.#L*"0D)9F]R96%C:"!M>2`D=BA`=F%L=65S*7L*"0D)"6EF*"1V(#P]("@D879G*R@D<W1D978I_*2`F)B`D=B`^/2`H)&%V9RTH)'-T9&5V*2DI>PH)"0D)"21W:71H:6YN;W)M86PK*SL*"0D)"7T*"0D)?0H)_"0EM>2`D<F%T:6\@/2`D=VET:&EN;F]R;6%L+R1N=6T["@D)"6EF*"1R871I;R`\("1N;W)M86QR871I;RE[_"@D)"0DC3F]T($YO<FUA;"!$:7-T<FEB=71I;VX*"0D)"2-A=F5R86=E(&]F(&9I<G-T(&%N9"!L87-T('!O_:6YT<R!D;V5S;B=T(&EM<')O=F4L('-O('-T87D@=VET:"!T:&4@<V%M92!M961I86X*"0D)"2,D;65D:6%N_(#T@<W!R:6YT9B@B)60B+"@D=F%L=65S6S!=*R1V86QU97-;*"1N=6TM,2E=*2\R*3L*"0D)?0H)"0EP<FEN_="!/550@(B1C:')<="1L;V-<="(@+B`D;65D:6%N("XB7&XB.PH@("`@"7T*("`@('T*("`@(&-L;W-E*$]5_5"D["GT*"6UY("1O=71F;B`]("1B86T["B`@("`D;W5T9FX]?G,O7"Y!;&EG;F5D*"XJ*2\O.PH@("`@)&]U_=&9N/7YS+UPN<V]R=&5D7"YB86TH+BHI+R\["B`@("`D;W5T9FX]?G,O7"YB86TH+BHI+R\["B`@("`D;W5T_9FX@+CT@(BY)4BYO=70N=&%B(CL*"7-Y<W1E;2@B8V%T(%Q?=V]S;W-A=&UP7"\B("X@)&)A;2`N(")<*BY)_4G1M<"YT>'0@/B`B("X@)&]U=&9N*3L*"2-S>7-T96TH(G)M(%Q?=V]S;W-A=&UP7"\B("X@)&)A;2`N(")<_*BY)4G1M<"YT>'0B*3L*("`@(&UY("1S=&]P=&EM92`]('1I;64["B`@("!M>2`D;6EN<R`]("@D<W1O<'1I_;64M)'-T87)T=&EM92D@+R`V,#L*("`@("1M:6YS(#T@<W!R:6YT9B@B)2XT9B(L)&UI;G,I.PH@("`@<')I_;G0@(E-P96YT("1M:6YS(&UI;G-<;B(["@IS=6(@;65D:6%N"GL*("`@(&UY($!V86QS(#T@<V]R="![)&$@_/#T^("1B?2!`7SL*("`@(&UY("1L96X@/2!`=F%L<SL*("`@(&EF*"1L96XE,BD@(V]D9#\*("`@('L*("`@_("`@("!R971U<FX@)'9A;'-;:6YT*"1L96XO,BE=.PH@("`@?0H@("`@96QS92`C979E;@H@("`@>PH@("`@_("`@(')E='5R;B`H)'9A;'-;:6YT*"1L96XO,BDM,5T@*R`D=F%L<UMI;G0H)&QE;B\R*5TI+S(["B`@("!]_"GT*"G-U8B!A=F5R86=E"GL*("`@("`@("!M>2`H0'9A;'5E<RD@/2!`7SL*"B`@("`@("`@;7D@)&-O=6YT_(#T@<V-A;&%R($!V86QU97,["B`@("`@("`@;7D@)'1O=&%L(#T@,#L@"B`@("`@("`@)'1O=&%L("L]("1?_(&9O<B!`=F%L=65S.R`*"B`@("`@("`@<F5T=7)N("1C;W5N="`_("1T;W1A;"`O("1C;W5N="`Z(#`["GT*_"G-U8B!S=&1E=@I["B`@("`@("`@;7D@*"1A=F5R86=E+"!`=F%L=65S*2`]($!?.PH*("`@("`@("!M>2`D_8V]U;G0@/2!S8V%L87(@0'9A;'5E<SL*("`@("`@("!M>2`D<W1D7V1E=E]S=6T@/2`P.PH@("`@("`@("1S_=&1?9&5V7W-U;2`K/2`H)%\@+2`D879E<F%G92D@*BH@,B!F;W(@0'9A;'5E<SL*"B`@("`@("`@<F5T=7)NL("1C;W5N="`_('-Q<G0H)'-T9%]D979?<W5M("\@)&-O=6YT*2`Z(#`["GT};

print $@;