IUBio

Bug fix: trev/pregap interaction

James Bonfield jkb at mrc-lmb.cam.ac.uk
Tue May 6 09:29:17 EST 1997


A silly bug has been found in trev. The symptoms are that when using
interactive quality clipping in pregap, "reject" has the action of
accepting a trace, and "exit" (to accept) has the action of rejecting
a trace. The bug does not affect non interactive quality clipping.

To fix this, rename your $STADENROOT/tables/trevrc to
$STADENROOT/tables/trevrc.backup and save the following file as
$STADENROOT/tables/trevrc.

In article <5kneu2$jgs at lyra.csx.cam.ac.uk> jkb at mrc-lmb.cam.ac.uk (James Bonfield) writes:
>PS. Be warned that the above file contains a very long line - be
>careful if you simply cut and paste this message that you do not
>insert spurious newlines.

Blast it! It would help if my news software could cope with long lines
in the first place (inews corrupted it for me)! I'm cancelling my
previous message - (ignore it if you see it) - and repeating the
correct version here.

Either fetch trevrc by ftp from
ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/trev/trevrc or uudecode the
following file. Sorry for the mistake.

begin 644 trevrc
M(PHC($1/($Y/5"!%1$E4(%1(25, at 1DE,10HC(%1H:7, at 9FEL92!H87, at 8F5E
M;B!A=71O;6%T:6-A;&QY(&=E;F5R871E9"!B>2!U<VEN9R!T:&4*(R`G<W!E
M961U<')C('1R979R8R<@8V]M;6%N9"X*(PH*;&]A9%]P86-K86=E("5,+W1K
M7W5T:6QS(`E[?0ET:U]U=&EL<PDQ"G-E=%]M96YU('1R979?;65N=0IG;&]B
M86P@=')E=E]M96YU"FME>6QS970@=')E=E]M96YU($9I;&4@>WM-('LQ(#`@
M;&5F='U]('M/<&5N('M[0R![,2`Q-B!/<&5N1FEL92`D<F5S=')I8W1]?7U]
M('M3879E('M[0R![-"`T(%-A=F5&:6QE(#!]?7U]('M[4V%V92!!<WT@>WM#
M('LX(#`@4V%V949I;&4@,7U]?7T@>U)E:F5C="![>T,@>S$V(#`@17AI="`Q
M?7U]?2![17AI="![>T,@>S$@,"!%>&ET(#!]?7U]?2!%9&ET('M[32![,2`P
M(&QE9G1]?2![>TQE9G0 at 475A;&ET>7T@>WMR('LR(#(@961I="!,0W5T3V9F
M(%-E=$)I;F1I;F<@7"1E9&ET?7U]?2![>U)I9VAT(%%U86QI='E]('M[<B![
M,B`R(&5D:70 at 4D-U=$]F9B!3971":6YD:6YG(%PD961I='U]?7T@>WM,969T
M(%9E8W1O<GT@>WMR('LR(#(@961I="!,5F5C=&]R(%-E=$)I;F1I;F<@7"1E
M9&ET?7U]?2![>U)I9VAT(%9E8W1O<GT@>WMR('LR(#(@961I="!25F5C=&]R
M(%-E=$)I;F1I;F<@7"1E9&ET?7U]?2![4V5Q=65N8V4@>WMR('LS-"`S,B!E
M9&ET(%-E<2!3971":6YD:6YG(%PD961I='U]?7U](%9I97<@>WM-('LQ(#`@
M;&5F='U]('M[1&ES<&QA>2!397%U96YC97T@>WMM('LR(#)]?2![>V)A<V4@
M;G5M8F5R<WT@>WMC('LR(#(@;B!39714<F%C941I<W!L87D at 7"1N(%PD<R!<
M)&4 at 7"1T?7U]?2![<V5Q=65N8V4@>WMC('LR(#(@<R!39714<F%C941I<W!L
M87D at 7"1N(%PD<R!<)&4 at 7"1T?7U]?2![961I=',@>WMC('LR(#(@92!39714
M<F%C941I<W!L87D at 7"1N(%PD<R!<)&4 at 7"1T?7U]?2![=')A8V4@>WMC('LR
M(#(@="!39714<F%C941I<W!L87D at 7"1N(%PD<R!<)&4 at 7"1T?7U]?7U]('M&
M;VYT('M[;2![,2`P?7T@>U-M86QL('M[<B![,2`P(&9O;G0@<VUA;&P at 4V5T
M1F]N='U]?7T@>TUE9&EU;2![>W(@>S$@,"!F;VYT(&UE9&EU;2!3971&;VYT
M?7U]?2![3&%R9V4@>WMR('LQ(#`@9F]N="!L87)G92!3971&;VYT?7U]?7U]
M('M396%R8V@@>WM#('LR(#(@4V5A<F-H4')O8WU]?7T@>TEN9F]R;6%T:6]N
M('M[0R![,B`R($1I<W!L87E);F9O?7U]?7T at 2&5L<"![>TT@>S$@,"!R:6=H
M='U]('M!8F]U="![>T,@>S$@,"!A8F]U='U]?7T@>U,P('M[4R![?7U]?2![
M0V]N=&5N=',@>WM#('LQ(#`@<VAO=U]H96QP('1R978 at 0V]N=&5N='-]?7U]
M('M);G1R;V1U8W1I;VX@>WM#('LQ(#`@<VAO=U]H96QP('1R978 at 26YT<F]D
M=6-T:6]N?7U]?2![4S$@>WM3('M]?7U]('M);F1E>"![>T,@>S$@,"!S:&]W
M7VAE;'`@=')E=B!);F1E>'U]?7U]"F=L;V)A;"!T<F5V7V1E9G,*:V5Y;'-E
M="!T<F5V7V1E9G, at 5%)%5B![>U=)3B`N=')E=GT@>T9/3E0@>WM334%,3"`M
M;6ES8RUF:7AE9"U-961I=6TM4BU.;W)M86PM+2HM.3`M*BTJ+2HM*BTJ+2I]
M('M-141)54T at +6UI<V,M9FEX960M365D:75M+5(M3F]R;6%L+2TJ+3$R,"TJ
M+2HM*BTJ+2HM*GT@>TQ!4D=%("UM:7-C+69I>&5D+4UE9&EU;2U2+4YO<FUA
M;"TM*BTR,#`M*BTJ+2HM*BTJ+2I]?7U](%1204-%('M[5TE.("YT<F5V+G1R
A86-E?7T at 345.52![>T9204U%("YT<F5V+FUE;G5S?7T*
`
end

	James
--
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/



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