From d64f8a89a9af3e9675f348d00584d380d9327a3a Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 9 Nov 2011 15:24:29 -0500 Subject: [PATCH] Instead of the SelfScopingFeatureCodec interface, pushed this functionality into Tribble itself. Now we can e.g. determine that a file can be parsed by the BedCodec on the fly. --- .../gatk/refdata/SelfScopingFeatureCodec.java | 48 ------------------ .../gatk/refdata/tracks/FeatureManager.java | 10 +--- .../utils/codecs/beagle/BeagleCodec.java | 2 + .../utils/codecs/hapmap/RawHapMapCodec.java | 4 +- .../utils/codecs/refseq/RefSeqCodec.java | 4 ++ .../codecs/sampileup/SAMPileupCodec.java | 4 +- .../utils/codecs/samread/SAMReadCodec.java | 4 +- .../sting/utils/codecs/table/TableCodec.java | 4 ++ .../utils/codecs/vcf/AbstractVCFCodec.java | 3 +- .../{tribble-40.jar => tribble-41.jar} | Bin 300819 -> 301217 bytes .../{tribble-40.xml => tribble-41.xml} | 2 +- 11 files changed, 20 insertions(+), 65 deletions(-) delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java rename settings/repository/org.broad/{tribble-40.jar => tribble-41.jar} (92%) rename settings/repository/org.broad/{tribble-40.xml => tribble-41.xml} (51%) diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java deleted file mode 100644 index de781b839..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/SelfScopingFeatureCodec.java +++ /dev/null @@ -1,48 +0,0 @@ -/* - * Copyright (c) 2011, The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR - * OTHER DEALINGS IN THE SOFTWARE. - */ - -package org.broadinstitute.sting.gatk.refdata; - -import java.io.File; - -/** - * An interface marking that a given Tribble codec can look at the file and determine whether the - * codec specifically parsing the contents of the file. - */ -public interface SelfScopingFeatureCodec { - /** - * This function returns true iff the File potentialInput can be parsed by this - * codec. - * - * The GATK assumes that there's never a situation where two SelfScopingFeaetureCodecs - * return true for the same file. If this occurs the GATK splits out an error. - * - * Note this function must never throw an error. All errors should be trapped - * and false returned. - * - * @param potentialInput the file to test for parsiability with this codec - * @return true if potentialInput can be parsed, false otherwise - */ - public boolean canDecode(final File potentialInput); -} diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java index c99aea254..c41444ef3 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java +++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java @@ -30,16 +30,12 @@ import org.broad.tribble.Feature; import org.broad.tribble.FeatureCodec; import org.broad.tribble.NameAwareCodec; import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; -import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.help.GATKDocUtils; -import org.broadinstitute.sting.utils.help.HelpUtils; -import javax.mail.Header; import java.io.File; import java.util.*; @@ -159,10 +155,8 @@ public class FeatureManager { public FeatureDescriptor getByFiletype(File file) { List canParse = new ArrayList(); for ( FeatureDescriptor descriptor : featureDescriptors ) - if ( descriptor.getCodec() instanceof SelfScopingFeatureCodec ) { - if ( ((SelfScopingFeatureCodec) descriptor.getCodec()).canDecode(file) ) { - canParse.add(descriptor); - } + if ( descriptor.getCodec().canDecode(file) ) { + canParse.add(descriptor); } if ( canParse.size() == 0 ) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java index 413848543..90d305d73 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java @@ -249,4 +249,6 @@ public class BeagleCodec implements ReferenceDependentFeatureCodec getFeatureType() { return RefSeqFeature.class; } + + public boolean canDecode(final File potentialInput) { return false; } + } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java index f4633b2ce..d9f16c353 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java @@ -25,8 +25,8 @@ package org.broadinstitute.sting.utils.codecs.sampileup; +import org.broad.tribble.AbstractFeatureCodec; import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.readers.LineReader; import org.broad.tribble.util.ParsingUtils; @@ -76,7 +76,7 @@ import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.V * @author Matt Hanna * @since 2009 */ -public class SAMPileupCodec implements FeatureCodec { +public class SAMPileupCodec extends AbstractFeatureCodec { // the number of tokens we expect to parse from a pileup line private static final int expectedTokenCount = 10; private static final char fldDelim = '\t'; diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java index d4bdb5aa9..0f2b94e63 100644 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java @@ -27,8 +27,8 @@ package org.broadinstitute.sting.utils.codecs.samread; import net.sf.samtools.Cigar; import net.sf.samtools.TextCigarCodec; import net.sf.samtools.util.StringUtil; +import org.broad.tribble.AbstractFeatureCodec; import org.broad.tribble.Feature; -import org.broad.tribble.FeatureCodec; import org.broad.tribble.exception.CodecLineParsingException; import org.broad.tribble.readers.LineReader; import org.broad.tribble.util.ParsingUtils; @@ -52,7 +52,7 @@ import org.broad.tribble.util.ParsingUtils; * @author Matt Hanna * @since 2009 */ -public class SAMReadCodec implements FeatureCodec { +public class SAMReadCodec extends AbstractFeatureCodec { /* SL-XBC:1:10:628:923#0 16 Escherichia_coli_K12 1 37 76M = 1 0 AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGCTTCTGA B@>87<;A@?@957:>>@AA@B>@A9AB@B>@A@@@@@A;=AAB@BBBBBCBBBB@>A>:ABB@BAABCB=CA@CB */ // the number of tokens we expect to parse from a read line diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java index 1919ccbf0..97c15fbb8 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java @@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; +import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; @@ -101,4 +102,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec { } return header; } + + public boolean canDecode(final File potentialInput) { return false; } + } diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index 0e0cb14bf..3377172dd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -8,7 +8,6 @@ import org.broad.tribble.TribbleException; import org.broad.tribble.readers.LineReader; import org.broad.tribble.util.BlockCompressedInputStream; import org.broad.tribble.util.ParsingUtils; -import org.broadinstitute.sting.gatk.refdata.SelfScopingFeatureCodec; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.variantcontext.Allele; @@ -20,7 +19,7 @@ import java.util.*; import java.util.zip.GZIPInputStream; -public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser, SelfScopingFeatureCodec { +public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, VCFParser { protected final static Logger log = Logger.getLogger(VCFCodec.class); protected final static int NUM_STANDARD_FIELDS = 8; // INFO is the 8th column diff --git a/settings/repository/org.broad/tribble-40.jar b/settings/repository/org.broad/tribble-41.jar similarity index 92% rename from settings/repository/org.broad/tribble-40.jar rename to settings/repository/org.broad/tribble-41.jar index 7f68b4b365817bcb3bcae230d547ed8559e36d5c..76903f007552b51d801c3b77e61623cbed774194 100644 GIT binary patch delta 10131 zcma(%30PIt*6R%1bGaM_FN1)LA|kW1sfZA2Dk>17IUy)0C<2NTPKc=~PQX#OWr-H4 znVCj;t(Qa3*RyiS28*&BdX>I@Q?toen*Un+oXh1>|NH*?x%b_7uVJsX_F8MNy-_=0 z-F3+7o|!Jm763EA(s{*o?p>rM`1R0J{Odv}|N1qOzO+yw-UGh})=YVhofH91idy-b z{`HcNwp#G?477j*ehRc#z+Zs?mi37+L<`>QLvX7&GGS_d>7c@?Wd(%-wCgfrM*jT# z#Nx8VA;l$y{iDYV;89*Sx3F|>aem3L((-w8wYt6DTCVu3AZlZz7(vylrO0uJ1)d;) z0suqt8)X1d+K;_N@`DNI0C8Ng_tT+Z0XO`Gc;E%?5U%1_<#-~(+&RRmZE*8wncx zTWT4k4KZc0{dt0i_Pi+~N)~W&55ByK_ns&qiP_GvAt+JPHPbSItlv~*9w70-UN>)j z=9v1cK6Autm&idAz0*Xl$APTO&5aU3BWuW&0<;r;9oem!vZ?8N-vc_yj)32FlBa{} z^_gyAHTvLKM6y13&{@(4E-^(4_ki+l5Ak(g?Dm+24@^nBbv7?27ju-R4nsbbIquKH zyK%eye0<&>A5_i93+?8wou43Und$AT-m*Xx6e}>p6*|LA3w9+I)P5FqrDiCj?{YKD zHp3hXRKQ#d%!By~ETBDGXogBNEFzS}^m~Z~mclX`RVlEXrmJ0H1w2kOD`~Wfy4A$z z37T7Dfp~XVON-Vhu#V=})BFYtY=lijUu%Xs`mR?%Q($wGFv3MtX5jM3U)y!*`KDJ! z`3Qp%6s^D(0W5nZ6ymK(q?IptlNJfvK@M2LZB5wj!4fC|q+qYBT%ZUy$J zuoqrXVIRDxJ(JlfVL!ZtGOKU^#;Wi#98}>Djb5Ry30_s4kGg<3|14eZT0M*CnNr)?h{ zS{09Tv_F9PKn5!$;7E^Z4@iWr_)CCp(4Fvc+z&Ac*Ax?b803RE5`j4A`NEe|>-oZD zP!p^N^hA1rwnFD4Zopa0EkayV-<-Yz7or9_BBPEF37t^nC|o)Y3F4s-j*^i@I{wN) z2BUFiG72&aQeY0GLNz=LYhVa$z(lqUhCu^l!m}_O8WDRBV(*6>+=DT22FAfhFdil20tG@lC=%L3u@DUeidIX8n<#is7j3sFv?X28YO6)Nnuwc$)+ZWt zckb>6HE`#5^f6Q3YbYJ<7VL|DUc@!=pp!XGC+!OAKV4(k_F*EApVBS z=A#HQis_4O3QWbGf{xsU1a`-m>v$L6$qHy8`1V2hUjv%i+N%|pAg&Zla#1=H3e76^l(W*BC{P);|)2>KprLC?&f zE>nRl3)=rt>awXDZH64e8RLo@_!xELXnH(#6R4YLhDr3DOWkDZ@~F$Vkfo_Bpr3`7 z0PLsHa5{BG)Y0Lpz|5vi>*onxJ@}6j6oCJmg@;&^c50(f9A;V-Q)L1gDMEn~6-uE@ z0BPdfSQW})wgPihblJHo9ltDNF=qF?ZN611X6OYfEQCrG7Qtd9M)W1HRDoG4#tOoh zQ&$ZuR16hFS_zeil&HcgSgpbnG_{7hwNR-*4K1-w#lYF1(h00$0AW{02=&xyv_xdt zoau>E=9J|ZB(mgFlG!l5i#8xDR$FXxW5;p?bCXZ)r(!6je}Bx%5%}GS?|dZsslbmF z0lKhd!Lna_I#=`)zzfe7`}yIbT^Jo^74^*FK=Idd$G6u)ax5;Cnz}UAY3@Q5fpeif z_Wdw|24J#CfdF*;4j4^Q7}DJ_v8UkfX5ikB#l8@Os|u6M8cZ{F82SwueH71l0K*#? zx$k1kHenH*@Z(Cu1@DB>XGE#MJCSz?HD zutskE$ddw*?MxFRw2<9a9*wIi$8Epv3vk^R?;>GMxw~aQ9=3&VuG8z$A5Z>UA6!2D z0*`2I-N$`6X~XazMuuP_4Ux2VN&f7_JULoRj&apCG|z9Uz3_sb8Iqa{cn!=7qT~o| z(?M75{fm}%bX7>Y=I@WLN$v>=+M$af?8qiQ*N@<|vw? z%DL&%7fpf}j*9qpr*Qd}VX8P46AuY0x=}CO9;`Gmu5pk;vAvR#MFmDb4{Y2^7P>_6 zC2K}#?_DlSd;-=`ysyRjF07=uv@mQyn2IOmN)^ik9`ZQa02>uO>g%Wi_KJr(1?nm6 zH>-GZZq+Uy^F`aY({6pI^i`41=8uSJE9AlG+K%&4929`k`s84 z5mHYKEdisiO-*T}i>^4YXOwVGZLcXQMCoJV;Yc2imLxt+N53f*gsxiLwd^WdZX%}b z1z1b=#n5!Y#M%)HHVjh8Lp75y!QlM}^J6l`w1gRR4G%^c(?J+T7S=n#e3XWGAPg{s zrV(WU0fP%r0mUjLKfp|=C@@%oAqqUg`zox@05eYb159Zc?gXQBFf0$tH6+$+Gt#_O zZ5F79y+iMDt*j=uSWPd@h_-EM=Ai63sg=n@yX>fmUYiM+HYq7Q>YNk~UBBsSoX!#T zubH&dcl3K{^PRziYN1 zz-&KuHC^_vf6Z$9b+%B=^AcOUMo8i-zOhF5jprkqtxkALUwd(b(2M6dThjsI;V_PO z_ndG+m;3z3LX4Hq-TziN&FdB0={v$_9Lo0G75Z`D*LQ_-{%m6#>o4YZ;B!ZMh>8b| zF!@EW6U$}Q&Hm^^wz-!o?&6wKZtcY>n$yJ3J-IsH?r2E9g|@#1T%D~aMJxL*TYNxh z?8a!ZC&%*Zbigac8z9A-{cr-q%>ys{$E zBiQX(qQbf!6-})kq)4{V2Jw!rtIvz#i|#!2zTb1-m#^X@5Vc2Hw;VBuD0|pKUl;$u zlfCWR6XIp=7`Aub6K8T)(3h!g7Tw#dP;pjF(04cRA6 z*`llM&WGYz53cQjlHs5Kf;RaD*kpIvpM`xX2H5_%Dk{3anExeS;eKfQpYO#T{5iz7 z{*L&m?pM=(5x>%RH2t1dZ(Ig%a9kb{}W zc1g8;#-y@Hu1oq+>2t12mt)ddo%ZfYX_~%9{%Pq)-NnaVl-~E^c+oecGVTes?RO=Q zc6@HXtNgrfuF>xD8C{l$0QnWZmA2*%@_pUZ&B5}|x<=tfw@TL@x@Y# z`nw= zRY^jK=GDo>V#^I}4iWT~C_B`w9glZs=2C+;xD=sBVi4Mi<>Dk4w$+MwYqx*A;QQ2w z?uhB5olkXRFP9n%93vLFI-vaPK;~Lz@D3?M!0Snzf&j(%oAdu@>Yb&Lm@%o*&Bgv{ zte!H^;NOnDYiDzb*qj?;UsyXk#EnIk8*B6{N8sLcmO2}gUm5Dm7jV4vwsp-fbX0u! z_27=g-TXW;={}J&(TdgHF;@=fJ9ulP$Jq(EJ~h2$wVSB?ETN`y!*5!SO9g#G6Movkk1g&_g0oHY5Im*@ zY}O832;kAom)Kigc*%+ZMy-#-c$gHh9keOYqAEOJC618zO$v4&4cg zaZ-0+Skn5fF_?v@IcK7AgdV6>{p_xJ{Me5DzQEAMvJiFo^cMr@%{pK`#%(h~dvBwL zXF0V9yG;1qSUs{6`(U9Q$d(I&3u{D$xbdZ_)Tjm#OY4s_%v3(J-vmdwd{js za)f6aXJc21S^pXiWG6}lGmBng$ep|dK@VvyARn$0H-Y=5y^FrW>XI5g$k;!P)%SMl z_$j-EcI;S#U}AqPF?_{+De~)ium!HNaZ8P*N(oeXUI*>Gf}}e&!IizURQBOvdYRx^ zpR|H^T_*GU02_q^aoP1&ppH$ z;MyiKe#^Qi2Vsdot*>2M{BEo+G>A_8E_7ghml+D3sY3CZ14NcTSqNau{Y8Ivw92qU z4CWlEZ!bHn1RWx`L{JJ4Dd;xE-d`c}YaRQ6c%{tXyf~z#X3KmWA*HK1gk4!J zhO*>!qA&ZxF2x4~KcKaOw~+F^oVrs7(KU=MUTGMjhPHWUYfwgm*oob+!+$6Emi?_r z5$?qj-$EuCs|+T&s}L#ejTWRH3@>XYmbk)zUn2PQzw2G0JE8g{0I)WnA6 zif(M!D#Ny1blW+ChyTg8=Z1Fu@NN7X3AIrU)1nXl#3?$ngbzdun{-|bWD}n-IL^jh z5+gq*js_erfqEWu-24FFC>)>0>a>3mehLruq8@(U_!njRt8yF9U;8!7Tq8fio#LrA zxJ=0{wtTIez`j`{^NR<2K(p>Y>9fPv%6^>ViTu$&Zo+7!=A1mP{Yt1qILCL_BJG*` zBuE_lcBO0$Cs%by3H-5I|4j+b7A>*ar|}(QQjM_>B{k^vH|*2rqoo*jrp7SKRf2t# zXpkT*kWE-`tl_wZwym8DvUGy2*?1RwYMsIB<#otw=vW6Y7uL0#;_Rv%~^pddCdO!VcO63s`Y|J^rbY{@mE+oa#HrAh=R4 zsqt-c{J?#$MxXu(k3nkA2h7$=gRXY9q-y2&-5gf9QGO@>1nxPtUQR-PvD!i8&;Gf= zFvG*itBP_DRHW94zlLm}#;XM+jmgHAdwACf> zpUJ1Tp*Yl{oWweF%%Hw<6phw-lYP}q$oYli1}yWK9J@7nbc@7&q2^rC?)#o|3};oh(UkXV4QGlteD(Z4kR>%|f}r0FnKSET{zApd z>M(}l-Po>rIe?|SZD_)SaO`LOldACbkD7DvU+`#!pXV(r%)8#m7=h~LM~ksQqvouB zV;~Vlv66b(m-Bz}=BB*Yut1{bTz-uUCe;2s$S>EUfa5}GB9eu4z;}%(&Dggj4MAC* z2o%AV*k|i-R>)?;W-K7>k0JW8#H;FWx)464kBy2`jA<;VMM4ar-@_NZu z?&@6DuKx->g|f_i+`ao-WiL~65gt(RzfptV{r~^~ delta 9681 zcmZu%3tUxI)?fRa1Lxk$;r$R1?H2rK!)BM)j=Um|8$FF_PzH9BZ_F8MN{Xc7O zYdY+wAN2Fg9w93>01H6pDf4PQyUW4&dSa(|eI71ezr@l@4`+$K_|AOu+Vn0xBminX z_47QCXD(1e^eSfc4zhs^ek%B@5THUJkNlYp(cgPDK(~(#(EX%QdXw}Y#`NuS0<-BS zr>W85Ab~poK0U!pyuI7}L)%+kQA-(3*3#XYE{o25&EKGudj4WiR`@na zf)yGtSP~W;%*n26mI0`x35(WtifVZ!=uJalddP2vz|^p<2IW>nh0!UE$uK&{;$)-q zVZwY>xSP`J2{FsUUeDS@=db=r4?4eYN9+xy*2bGB|Ubct+hcHPbi~F*Qv0c=o^Us zyb9$iyr4f>9m$W+X4aMmBQG;`CeDg#TfQ0n4hukjtO^?$*s@m4np30m1~Cw;K`QjpU=vhmPzhBGShNP4VG9GdrAubaTF5}1xuj@$$($uBRBKQJ zwJL1YK!-Y>lf?q{D}{b2&<(bsWE5tV2KB%-*bX~X*r~yb@Lw9d1iSRZIWb8M(1-?U z&;;W&*bRTwpqY9v(_;_3qQPExRfB!7UxQIFn&0Yy`i~!0_3*J)%K>;zgM;w8?xPaX ztEFIUhTIh*F)-1XjW{!TgHILv=pjD4>-WZocZo+D#ThVa3iv<*_B1ixOTSPT;inuz zf&?_oU6B2C>$XU@UZkL;OFat7R31mVU41kUB6h?Fi#$+foz-aV*7&<-*UV*W20LFm>rB1^{_!~S6U&AE$ zAD9e3!BqGa^5A!vVP}|n%opaePB4$f!vf*L26U$koqY^VQBk#ullQ@AGor-fXqJj< z2cjXwJq}tT?CJq>5uYuIQPT?!c)zE`9rrQcp$ z?m-w)>QQVJ(R&ija6>a+!X!w?fCfMvjK`jeCRf4)>{(F52277wu;K)3FiB!@702PI zNyzmOOVAtKAEHGbDokd5RhWX|$FQp~l`&j%{5b_+0DAzQ3?CVc-393$PCE@vP|(ak zpMj97U#$zuQaY}Jr*J9v%oyxVM-OQ2a*-}Up6jO|bLuezZdq=ChXCN<1)DuZ zXYX>|B03psztsc)r`(C=*-I5mkn>|nAHv%YXRb)ZZ)c*7=S`G@^|hO$?DaO>?!#=j z3!k>Ya2uxPNDGXj_h=g~Og24oR2XZ+K#ilvGxQj5feAEbq7@@Ii5`=QJcS-p=`qa$ z)9IZ{k34$JpvO!b%p#zlML=(bxi-Dq7B4UAE>K~i3I!@GYDwF&jQR8yzY+1rivNoA zW7Q{n#zA)tdO15l5VOJaZxoYylM z@fJu%-nB`07ShhVGo(p#3W6==9fsD>gSqU6bb$Lk{N%Uv%xw>Z4b!0$()!{4$UrC< z2%T~7b-~RVhXB$Gh9i)Tz;qdd`zjme;1;&y?%asGsuuTE1Ma)M$T^J3@-FVOj}VYA z;ugA!aPd8En!5av92wk$E<5R!tS2n2x&Zd@#S zX&*}~>wmArimK9^e{f9fW0B;ZdX-{rv2CyNCJ5k3SyHs#c*d%=7R*#fo_{4dNI-@B zex*^g)qeP$(OGlmRe>Trd$1JEM=w`w!7d1t*)aUpsIG{$U1j}z|6m#s-}3qw-Hkf& z%S*FGM<4k2$3^Yu{^Gjbn-IdOC5a;R;k6*WoO#>#+YtW{N8(K!34)0hc-96%Fv&td z5(HDM$egOeG?ie)1D>%El6Vl3c)$z`;fM!SjWz<4AOe#h1QYz|%vT|wemIN9g|G;L z!Ujc9OpnFH8-$f(No&!#43^tq1+26|2&^KFxV@jVz#1E-RjEn^V;qszs!*oFI;`M| zXDnH&53KGiN<{s^$bKz<|9TAb!2$UqaRv&r?Fd*c`pqi=3Ai~mOv=YGf3T=SfWgiH z0-17xt`dYHfiSomxlg(rNMViUU#3Z+dfC-+$)bkb1eFXd5e4~$b0X3sH2j>FYq;qJ z0Aa5hYE*)st)Np4>PI|Xg*t+vdJQ;i*R!7s)E{2+)kj~m_T54Bc4edr4TNNkDl`#i zw+4TNW))sG>&GP6tHG;~te?LertiNNA}7H{iZ(ByRUh24R2TjKXqAd|1M4D%v=gliY2wi~r_G2lB|R-8{#D3W zs{Zcvadw(+Dt=9tBb25gP`M%CM`8KZ55@AZZcaydk+9O*g4_EE#E%k$C)(r+!b}8$ z*b_QAH6~KV+bAHK*e%Qg`p}86Hoio3^C#^L_Wk%Il>6> z2xf-osfdgW%c@aiF{)@+qlFlt(B}7~c2QGI0~nTKV@%nOaMC8(ds@4YNlx3*lWYWI z3fWkkT7q#d+qxz5`x{oXXn0IO!`wToB`*S+lS)u@B7R~L6ODqQ_`ZKj$S>)MG|DkK zhMjj4y`%)TT9hV^13g(lv=A-Wz5HJ{aOdC91V+`bWPy&~#<1T-dE&S~m0b~N;rJ$x zZ5QWR$EulZyql1nJECYyPY*n-d+?vWl7o3oJ_~jD&S(8a+2hDAVQ&cx=$4;FUh?2=+ZDM@{PC5o2VuK=tmhyA# zbHk(QU$6u}L94vZP8riqy2CCBE-!9GeDn#IJUigyy`1|>XgEMcdENtN z<@>&1UXH)qV_n0Ak*lz9xo|>ct^N2%|AD?_y^5!p$mwpn8R!xw43#r2sq#gdE zH)?^@BUJQOmrLnJRNm92H^d5&k7pjRH{+D>UmvHQEy!=mtc_mri5-DhlbL6WAZTv*}l;K8no*ZN-?mt^L z*2OVoi9A^qvETP*{HZ&b=XW$RH;fmrW}SHa3o?derTnvz?cbHlK1L4Rua#%HiD2F- z4{h0uU_q@LPtB7<_`_<&+p&YooC(cG&)QioR)o2+d_a~G#?P*nG@e_dxH}f@kn>}O zGnd|%zZ8bQbxb~E7+(INJXd_r9XC(Q|7)c9|9mB%^%3J7KgvahQStX=FJD1R^H5%v zg;5hP_3LlPjYqAQVbqlXCD0M>tyCKh91c<5Ft+;KFy(=<26MxepN#-bk5L{P+`KrY zT5z!(h~|w$6f5rn4@eooV=T-*llJ1GDwhKcZyg(ThL8JpWm3=30i&4WJ-ul;E=8*Np zK>^~*uW^CmCq}#62)2&J`?xZP(mI+h2>Cdt$oAb&zT6*kfm)o4$d~S|BAE-75MlGw zg-RD`ip9y$4|%xroeLEKS^RZkzUV2>NQ~@cuVRs z4WChnCd5PterA#%KT>Gg_AxOIM-zj4X0WdMxfpkzQe?W6S%lo%-Gtan@qxU)$Q0X8 zj9=rC5yO9Q5?L`4XQd)BK(86(!PARPH6w|!OE9*68^U?9spSCC@Ae}BqW^+Fg^Pci zb$bn7Bhpo(IJG&wY%bfKVQTl~6BnCW3KpXluOZH9_02;)cndO(RCCJWJE*nq13wPD zK3qs#DOC7_#b#_>?qgd=Q(}gW5To&WmOs73oOt>YoOr`zlR;O8s$M+Ro%<{`)$Ltb zo%AuTHML|Hbwj3^lXv3xoa($wP~Eio#NY!;lmwBQ@{&ir+B zNLceesR*tY`pv6@&Vq4v9WrjbEEssE^6Hp=%aGk|kIA;^-@KvmJc?P$I=*-yG$2W(pnxsXgZ6%%`W!(UFgAjW9C3 z^fTg%Lml^8Zh9NG964{da{7ol_7>0i+7GuLwZ1NMBwuXRp&$D)ux(%boAlIQ<~b{r zutxyElZse8q^SJTiuS9z?KZzUkA*yw zb(`m`RGtzpwUx0QbKvQpX;d8lYNa{bt(8g_`B)U=IfqzhULzqyC$3WbBIz5j=*-Ca zG@OW9Hy2Oz?xsLCV-}v9z})#6yP^rHKc-%f{_iLNYE-E^|C-BudzeyZRw=P!Y+KPx z7rD%gVI^(qcHJA0BYmO~0U_m?q0Z|AfuAbbq7*U5>Lfd%UTt^n00@;~3 zvBw&7;)pdkap6Y6!>VqLnTSP1e$5~!aEEjBX(I2d6{8clU1xsWYn>TZ&#(8cx`t&U zwI^JrE^H72N!(@JgI(qeWM%JG1y#F^ZnaGDvFQ%1=q6G+f&cu z7TEbK_bF2%A4&AKqXmcyE~m%MWfz3RP+{=oGE^}Lk6TAI@&d^eZfY#SfN z&kjZ-j-yZ;l?UnsY%H&sRNxtLso#T_+QAUtIb&0cS!VB2x0W7h2*M_P?S@AP_% z#W&9wW~c0sED5fdof#B!&}V=@0JRJk7fmZaisW~s8=?$PSvkXAeR<3VynTbdET^5EcNHR3@RR?Jh|0b{cP%#d9e=5Z)$^G ztnzDU9iPgNV%$VDHi$+%7{5?%8v6sWj=XKK)}D~k`1c!4R>2F%x^%pi)lEo= zHBFs$ZC?Z;95uSBaQ-!yz4vkJES@}QqY@?z5Wd8p5v=-ilIJ6-`^m7BPd~(em!US= zsSV%FWpi7lLixFkN>8Eh;YKu#e`-vHhrc92ow130xoS{-{v(C(1Di}=J|Na_*9=y~ zcTyxDij}bN<mQBr#R?w0N-7j_3gMe8P?i05JJ!Vt#kgv?MXX8x zX=O$5BX#C1Hz69E2)*`!H-p$6Fh(PVqGP|4z+&mW@|3{VhoLc zT7)!xGb(s@JQ2F`_j}3KUP-eGW|Wk4D6KO;>DTwy53m@Z=DNu@PAB2c{Pbq?DD^w3 zY?^6Mdltwxp0UNWsq?z)Rrs%#^e>m<-*Lgn@8+`6&(o+_e)ckchQ8Zurc8b{+Bu`fn75%?i4y_&h^QyG z8B{!si^~`uR)f^-+*p`%t0fOQgB$4;^4E-$+i@CdaW2zl9HsHbvGOBSz`F378a%RE zYn5PO@uE=M>|hK9HP=e+-zWIMT4kUZ_1)~ge)|v*sU^8g@XRS170K70m#zGCt?Ad* zTC{ce59m6Utp~5nQYu>S+kkr2@xG1@}kRJ4E|tY(63nHCK;= zIvcW$p^C;Mx+!k_fo}S?<3@Gf5&Q&Eb1j=rb!jKGGYq|$UT5x~MRn-KsjybQA8!mt zFWz(VKPLW(D8aAarihy|9=;8UAI2I&Jp%AnWBN8TV4?_~7)Puy{@ONkmOqg|jY+LZ zLxH?_yrH|f*^E`nKSF;xiPaM|*9xk#r=cpZ-b}<&>_|HY8`RukiiIDqcP3)%ok>S6 zAB`}^*NjrU`HiinRf!x`?HFTDkfV4#vJOAlvex@yIH}R4y7RBOYkmS*<9VEIHxWH$JI;1r5F+@Z?MjmS@OcQx@PBSh`NjYM diff --git a/settings/repository/org.broad/tribble-40.xml b/settings/repository/org.broad/tribble-41.xml similarity index 51% rename from settings/repository/org.broad/tribble-40.xml rename to settings/repository/org.broad/tribble-41.xml index 6a01b3790..6ee8bfb78 100644 --- a/settings/repository/org.broad/tribble-40.xml +++ b/settings/repository/org.broad/tribble-41.xml @@ -1,3 +1,3 @@ - +