From 7897d52f3208f00c6012c63e8ea21936f26f600d Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 4 Apr 2013 10:44:40 -0500
Subject: [PATCH] Don't allow users to specify keys and IDs that contain angle
 brackets or equals signs (not allowed in VCF spec).

  * As reported here: http://gatkforums.broadinstitute.org/discussion/comment/4270#Comment_4270
  * This was a commit into the variant.jar; the changes here are a rev of that jar and handling of errors in VF
  * Added integration test to confirm failure with User Error
  * Removed illegal header line in KB test VCF that was causing related tests to fail.
---
 .../VariantFiltrationIntegrationTest.java     |   8 +++++++
 .../walkers/filters/VariantFiltration.java    |  22 +++++++++++-------
 ...nt-1.85.1357.jar => variant-1.88.1401.jar} | Bin 555516 -> 556173 bytes
 ...nt-1.85.1357.xml => variant-1.88.1401.xml} |   2 +-
 4 files changed, 22 insertions(+), 10 deletions(-)
 rename settings/repository/org.broadinstitute/{variant-1.85.1357.jar => variant-1.88.1401.jar} (94%)
 rename settings/repository/org.broadinstitute/{variant-1.85.1357.xml => variant-1.88.1401.xml} (71%)

diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
index 9de190f5f..6a29ff255 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
@@ -47,6 +47,7 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.WalkerTest;
+import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.Test;
 
 import java.util.Arrays;
@@ -106,6 +107,13 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
         executeTest("test filter sites not in mask", spec3);
     }
 
+    @Test
+    public void testIllegalFilterName() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName 'foo < foo' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                UserException.class);
+        executeTest("test illegal filter name", spec);
+    }
 
     @Test
     public void testFilter1() {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
index 362b49f68..83d4d81d0 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
@@ -186,18 +186,22 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
         if ( clusterWindow > 0 )
             hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
 
-        for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
-            hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
-        for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
-            hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
-
         if ( genotypeFilterExps.size() > 0 )
             hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
 
-        if ( mask.isBound() ) {
-            if (filterRecordsNotInMask)
-                hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Doesn't overlap a user-input mask"));
-            else hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
+        try {
+            for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
+                hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
+            for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
+                hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
+
+            if ( mask.isBound() ) {
+                if (filterRecordsNotInMask)
+                    hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Doesn't overlap a user-input mask"));
+                else hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
+            }
+        } catch (IllegalArgumentException e) {
+            throw new UserException.BadInput(e.getMessage());
         }
 
         writer.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
diff --git a/settings/repository/org.broadinstitute/variant-1.85.1357.jar b/settings/repository/org.broadinstitute/variant-1.88.1401.jar
similarity index 94%
rename from settings/repository/org.broadinstitute/variant-1.85.1357.jar
rename to settings/repository/org.broadinstitute/variant-1.88.1401.jar
index d341e1cf5cdc9f202ea7e51ef59c6334c83040b9..688c6ae17c73fdb788c2c83f32a347bbcfd3870b 100644
GIT binary patch
delta 9784
zcmcgSX?Rpcw&!-=+g07U**Xv)kfZ})%O3V62}xK&Ac2G}gf$_AHDrOX3D^X5a0EsW
zqzH?EqPU=Jl7_(%To4%?k#Rspae~VD#)W0nL6Il#oT{6J`TXAZe!YC$y62ucTb(*p
z=TtR!zmHn~bCiGHaJ%jT-~dC%KeW-m3(p$=P^Ol(BWz>ptfU^@<EJGh$M@*bJ3cu%
zw@0_6?w&3gm6c_sp6v3Hgs%QBe^(R#VC26TX{Xoi1bS`iqV<yRVy!>DkL=RYGzrw(
zR@ws)lUcTTez*P%pg$8u=WJ1%^7OzXPdcVDqB<PVb)ck<%kQmAV8+<n5fUh>eozUz
zy6`)v#9Z)RQ^4`x+ZFN2^;`U8*Z5kiEB)!#Z6s#mtA^?-Ib*Spz7VP~WuMlCNScl}
zOO%|oKb%p(*q=iU*;W4QYQvwb58V7!k8m9zd{g4hBwvEAB}hu&RIbfb&{<QP8ca;S
z*a+>ET|(ERv~^u1v|^Z6E{7_v=W8hv6+cQ_Ck+s<mTH3~N}r(xb(B!6wVLLUP}>)^
zdD39t+B)rCABkIkLpu^9p@CsGkJ2?G+?Lo?;<gU49hBz#hUeIRRQ5l<t>*lX==~qX
z!81m(D9YuXe0xXP?n#?`&rYx<XGq@5+ilA`NvQA*+YL*~J2s|tj6G-jt0{Y9KC)Ff
zB(&o*+dxM!`6&LN!;@wJ(335KU$OTWL2K-OzFyaCBb1~yU)zeeO0I8K*;^({$o`5w
zLrKr_*{l0X+-o=OwF)=k2YaUS@2;QhgBA4EUAr!!qu2Emg^D-yBf6ZZ1@%Fp*X;n;
z#jU&cLB3>{e$OsDPDUJ=un#--sg9Ze{g_gb;?@T!DG!F~nM#VjYUev&An_N9IJm9;
zgCgdU`gIwPzMnn%m;Pj}s87&yq}hpy`Wz)`M|V9eO5%=>(bp@6>~Z?rPU)!3JzrgV
z0#_nEIigrMQbo~3?)Fs_>APH#D|oIx#ZS`SC`-^jLOOazE83NtbS@@O;=#U4i}cSG
z!-*Pwgo+Y#z1~O7QC6)UsA8z_xc-t{Gd|~=dVCA1qVI>gUGWaMsvirIxI4G>ac&8X
z){W6h-t&P*xEj>i5TjJhV{#kgupGPZADxWXRPVl6<FtzPiZRBk1EiFM&Bj+sTkGeI
zL&^>BzF;^M$HkY8@0C~29X2j2$<G}#rYgwwnz2DaJKt>Jc=n9JxRiYGyx}#ZgQ8Pb
z{JIBMCOx_2pdMo7B_mWkHk&(q8!j3zDrISxjkPLZ->o;!DpR(8ZcJ1L{QH_wpakb#
zH%g@ojvjOD8X<K}80q+<VrZ4`$P6W%m^9PTPj=SMbPQ69sJ`6sR;k48`<r8ja_Eq2
zjy&b$+8d5uYDUjZ8as@+0qBVrSFf^;n*uu<KG!dfR?7F${%oi+x+0j3Q){bg&Sw9Y
zBLL{>Cz(W2A#)4=)-2H5!3jCAgPNVxJW0(iC+vnjE`*+9@HB_LE@1Es^*rl@JlN;L
z?&n<aJiI{7i!Rs?FEM!81wn9t!$Eo<qUJC)M@ZN!E*K3*IOMxv1RNzvbtK-$yl{-e
zaSngvaDv0DF8C9?=7N)O$`4+LH#ofMf_Cs0i8#&SZF-+^!aH!5nm=<mNAGv3`3r~l
zTyP%Vr{)5KzjFAS3zFd(7hHr(3_j%WkrTm>N$+I_pK$op1%31384g!Ce8%AKWLrJy
zyUO8ndVj&;OAgmK{DZ?+4F1anS#W?1`zI;+n&`h_@GVLFj=^;XHyGR$7jD`@Y;en0
z(S~(%1bxfk7=wQ?xW(XmG(#MUWXrX`3vC<gEXI1+k;t(y&V-57OoGWK6v6}sKbY_%
zOfaDg=55iDa6}aA-+3|o+k^rbZ^CW($%LPwlEEDlet}98?!tdF_|=4a8i<Yi^f1GO
z#jr@6k7BLcYno;=v9X()4#lQskmSXh!-Od?)r7T3m(fOVDI(gl_7gQ`YFu+N&1GtS
znu$i6n!gsHftF#y<FLtuH(>&PWts3cS^6(i3k0vJ1%Vf_38ofIUvB!c#V0c@#MD}7
zEln*HDn<Usj=`e7J&Sj?B5Z37LPXVrju6qc11sQdX!Nx(Pi!pII*S7x*dM)NWNurn
z9ZF6ywQwy0fiw*g#|<1Zw6u77>HM78<)!^R*@HYK#pUG{)t-`y^6KK*<(}g5nOJ>H
zn_pZqx3qcza;5&?xICp*3yaGZcoxi_S&p7u5Y58;BQ+0M8)d>et-UxDZ|{xH-2y@+
zcjAdYXGb>25Z!j;Bvr+*)!rNo3Jper18jgZ3xIE&Gx^4;m2aGE`NsLix0|K`-@(XN
z1jX1+!>>eqYxp)|UIFbO0yZeY)*+GoVLHO5B7jnufnOTTL}oj3Z#p?Mv~v@2%5M_S
zg4xJ2O`M80niHq~Ch;7YD~WH$vgX8Tze$WSD~aRdSX8$rGX^vx4zg@6N4pKM1*Fqh
zE1**Ht&C%x`w(9M*s;yPy(bf$Gq4$dXfu90V8{`7mE`_=9IMt!#F%*2!Anl^ppX>k
z4D)dgZ1`Pbu@bZZs*#6`U|@97HAet`E`&uS2$2Jjfu_Je<}idF1wF=g6kLZ8p{7Ea
zSB$*Va4Jfgndh%`xIo86xP+u_Nnk_Ks_X=om`hfr;Y0%TZnUMhj1^MWTSg06+MD(R
z>4M(0J)khcQLGqJ@KO>iPA9Mol*|%YY%|G8jgpfZB`2Ze3DO5ijgpfZB_}nL`~XSz
zc@x=24Mhhhv&GVtLxJHk?*z+WIhn65X;6aD3N#SSN9aNDk`jc-R68VVS+Ejn(Bv^%
zG^|2816JcuD0)@jL)b@?5Ci`AU=}zSJj~#C4AwAsgu(9-Mx`PCPJgG<oiLWcqn*Rr
zp$go$$WCOujdMW0+a=<=vC+wzJEIOVw?QB+9rr+lYr+2n^euD`@<IQT5<9pVc8FNo
zjd{Eja-G15?d!Przk!MFEwtt|M$X$fs59^goW<?w&+sJf{WOPa`R%ftKm*|5XxF`!
zvt>&h(7J||tR<imD3EuZfUH6v49$skhm#G*A=?fGhrtg&^g0kmch=84EH~C25vRIh
z-I3U3Z}{-whfRH)fFP6<jEJy0XjKOxZX8cY>@gUQuR3T+`-Lv|iv;jP_!64-A+&^#
zAssHm5cmW$)~7HEKEr^h$H831#q&81@(ZsV8Lb(#*BTiI0qb!BHC%#|;1BQ^`o3WT
zRo@2eqwxoWaTn5Y$_xVm#$Y3MV9vmnrs-j1B*8JUuS3o@FzowdPeD#@Ok5r0)<R1f
zo;MDgI_OvnOy38(eLs@h<v`pxAb@XiroY2Ex{jN}jb^sSG=w4s(Pp$z!~S;g1a6Er
zX_+6`op&JuBP*S@8r;1tn<!Q>S|J^^yJBAvul8UAQc4h^HrgMgj!;F?s3ToUR%6EP
zD^1GWs$`1ZJz0{BB_-i*GYOH65+d)H5T1^inQ|X0w!t>pZpZln2*cs$;cP(=#|kP3
z#-z8wqK3f-;Joihof&_)SH<xl0D6*r|LDnXt17a72-~D;*G0MP163O4jAE;u@?bq`
z;K|w>2EYwNB>J;1n>=oZIJL_W;A=C9-BT5G+i7e@Pf2VZ{JNkz0H8WR1i#0+Jl@A8
zMpko&IGM|wUaauqq0EWdY#ue`3@SKO(iT|7VZIBx!U7J}92Rm|#9^@uX_hcp>cWXC
zqvio>mN8gPJu8U*L4v&0EF;<2bcL1F)Noiu@6~?r5IpRM+rt{aG+ds)_rvB<25UL2
z^8*j8XYd$@jU@PS4x3!i0jdbUnZXkrwqWdX*vg=m!8WmGD=X2qi*L5Fv-)!E7jbdC
zz3*}@(`-RY8SFr*Xf1=CNH4zG&Q|#MfhSGq1wBmMlzXU}WycN{9nuGOVTh%eSgP(p
z0Lzsmv2zCt3;*A06GhUtiKKZUV!}`uEUP+~2~WY(CYGUtsrpDtgF!IZglrgQ;;Kd{
z7xtR)3_Od9JD9K!o<oaGD%2UgXo4)$cbM=p95CS^91@XsTd0Y&am0Rz!C|58Hd=~P
z-(yX-e<vFq{1hC~z~PxOzha)pL}iC$rPxCAXy7-fbV14d*_G9^E3j0;%BW_$y`}Je
zV>ra*C)oq4B+B2f=lMGBVt(2fh{BnS$7Pp*G0_g|n<RvjWvF+<@9xl}@w+E30`#ox
zL+9e#iG6*bFSh;g>l0iQw2_PxFYRXShQzvA9q?^n#=4yd$jx3abh~`uI2r5qYlboj
z6%%_DY%y_1!A`l{4*jw12BxUr&Du;$Km~mem4QXWa7e|qmxc*+0Db{Rj#P@+H2gyK
zh$o{7N=L|sT!6c*eh<fE$Et<FK>UaMqSK9JI8|i7tj<WM+8?r{=!Q~GiPmT`iB?u;
z-X`L_-z3IpAYv5RR5aFszbYD=n8*AEvreI9F%QK7&|o4?KmcYJ%AU9t2f4lI!65vw
z<EsvW|5NPbW?~~O-)Iz)me{2zmUh@=-1XgZ*C)Za^SfoPYEcWVNw`9^tOG<e-~0Px
zIe`n9Jg-VEC#D0M4YesJH_k>f&Q}iVq&aZlcHc1_qY@VcmE+`_bjuDirVc`5W!h{_
z>BS}kKuyNXW|GYY$zII#Bc*6M{N`KY#$Xhaw<2TShIS~j&6Cj59TsE9Oy2f42GKCx
z70tXAi90+6H(88n1d{;9`B2>EZDg?a0cyal8N5GP6M}^U26|9|o*Hu;@Jw_Z!ZjEX
ze;n{wR10Sjh}7T|c>3w>YJuBR_hCkJM-fLG{W!GOu!iY!0y-30;@r{L)dubD=<b9N
zj-ew?uMaw(j3xRmB&#cScnjnr3M!Cj6obAavAE(oTY?FL{D^7U#Og*T<77rRsKYdm
z>ZBp0lRi-&8rg&_*mtjoT*Ro%3N;;M{Nn;eS1iFgW+?>116XP-!_8wkI%);_&x=Qg
z8f;f#E?A94!W#G<QvpRu4|HKN9D^}f{OS;nrQ3KsVN*2ygtgB^d~>)d%V7;=euXt_
z61ty`V-#PK(+fq&su+s#P1DsM_^%L-mA}TI<Sw*hFx`=G8*&(w7U6RbBhX+l!y>?5
zupyek%%8Dm77DQ8@yiBtBs3TI4>|_gz=H{Gtiy?k>JPA?A;U8?5$JAs+cV6qa`J%}
z*gSP{6nU6sD%^A*%TV`f&%MQTb?0>8G#jI?rX26F1Dd)^KNPtmJs2Q8Sk&aQE@JnG
zEJ*xv9<PG%4raOww`a6-h6{Z((+SZqi=f#Y=J??m5Hoc&%yVH$RY6cCr-V8e<}+A8
zwAJ*nkjVtkU<t{R2_ADh&KIZL9snyiJjlVzVI_weVpzpswF@F3dnU<5h6s3wSRW>c
zjse8=2vK5!p9_!rVdanceLehvn#UMy@Pk;`NX_F6HZj=jd;NVj)iCk=@Pr1&%+l)Y
zL1N=r79s{*Vqx}Putiiwv$pA&V}yxYe|O5`Tkp?knC49^#I~Eb@N+T$o3K;m`)s_|
z$R1>3b-Y`=zTeiui2;*r!X9`^)d0U-Vj142A>V|(@C*s2T#VHK=3)f?e=aXL-d@P8
zFN=mi6JCV<ChlD?QR>eZ7k<_ww|vf+2+w1I(I##<V@x;z2TeExhZ!6(;T1TFzB6&9
zKV^asj!~h|%847!F%zD~PrCUKc=OTSH|`^LT~oQf@Hv}DT-;;y727Yf)A7+bg?Q<L
zQEej^$w)_EBTgmuo>;|d=%3!$_7UqpVd+|5@!lsa(o4HFty{`x{pBhqC>3RB5=YV~
zqa<P;PR8hL2O*e=yW=8FM=YgMh3SbH(vX4FeXwUS$|R|QG4XM@mmQ;>#|M6@3h0X+
zE-AJo1LG}I<_u*;V51d*h*wqwVqPC4$pfWjw4(%KDjm|y3Wdo+j2iJ!X-zg+BhG)y
zQgFQH71nk(jW-6V03*0zys?erjm1pbU22Mz^6hezD*I6%6-&f97^_0NrD-@y!?-0)
z*!NHLG}%`sHe6xx-dH!D7+cG7sSN_MTna99hxs5B%Oy-+ji`2nqH>990RvB^;Wi8r
zI$Dyq)LD5rF6|tw>vC}lMqt_>iAgOFH`Gy>u1Di?9U~p7N~ba!UKX;VEixu(KFeqY
zqNV8wt1^f%G^!DZ!Hb#Twp2eU7mh^TDhKxw8K1E(UbN^0L}0lRiTTG<2T?SDC_D+b
z$5$P6plZb~%~c1;0^Cf;V~th_k+}bp=anZ@Ezfh*OtGXj+M_U|5Tnsb!4`e0wMD5I
zOI}!kWleO$VKzD!9TkXY*g$!PrNYKI4xKbWlmd3qu~(rxQwGN@OBuW?W$^9@#8B3a
z?Wa>tj3YRJSm`UC$o*}&COb-X`|kZ&-;cG?eX}tI9X1uKh$0N(Vhq)3IFu4hFVpd^
zq!d%;tj4e&2ko)29gp0Z=pMS6q!3xr7=SA<IZndC2H?#am3U1Pq&TM_=Lk%w&;lHI
zwC;?0wYw0&ps42^B-T)UzNp#5LWT#bijhJ_Ras@yh=!6^MZ8Vk5YWY10n)jUKNf>$
zoa6peuCKVBRjAbV!Btize*yJn{m7Pu%hWb9?$uwvL-y}L<X>}i5k;*y6ZhQwzvVA0
z_d@vB>iqj{Yksu79e>Ccd;9Y~jX!0JFZ*-(!;FYZ;fcf}MyK#J32aW`LnLq|g%6iN
zY$~55fk#t$i3Dz@@(Kw|OXCwHa59Zgk$`7_MeH5G%OvLd0A4MD(sT>>G@Z|vnEVV2
z^G*XWAk)IsW%8wxrrSUZ^ZY<QM`A(;@!1ksHHc4?Kz##{HrT@KXaMds0ON;PU3Eiv
zq2zLBS*BKHS)+I_%c6-J%H@xhV%bn@T%Qi*V<lIQY+fvZt=U}ukhNtPpD7V@hFR`;
zf0$)y>TteJcD*~CmrEcu$0FXB!{<p%t6aWJ0#D@fxe~CC;L{{9YXn~+fiFhz2P9B5
z(sKM?M_R<`d6wiud6u8L<Xi69oX;yI7aPS_NMOw<i}<HemYg}GEt)G0K;9Uu>x~AW
z$5;#VYy;4GoP~L`0l3=$lowcC^#zvFqVd*9-yd)JJF(EB*;8nB1y8Vye`Eq*u56yj
z7fYaKqUD6U6ZwM@vtp9vv0o<fha_gzWGkR<Pv)x?%@oUHccxgFl~Z|*?9z)YuC+zh
z?1U9tN^6VxW0EFz8n2STu4$H>b|sb>qQr`8$8^h{HPfw;vQqv#$+e->QqgJ#e^g@j
z&ak@TXIemA12ABgHJm@qvL>$UY)jYP*_Pz!Io2p%n8VjffqmxkZ4$UR*BV!0nH3Ue
z%J?GLl|Ij6KQ)gJlNkSU%d2b3d6C3?U2d(0Ar;mlc-jKCRPynXWMZWiv!^Th3c39>
z{mv@#sw}pbs(4%5>%Bx&HIEkO)0k7-uHy2iT4Bz|uCrOHD?OSAiOKW1+k@Lq=EX%J
ztyf|}Ko4c`hQGZvQ%5NJhzA@&;>AT4{hjc2bCU4pnx6aVdyZE0-cc-6Brf2lv^{MB
zsy;D^x?<#gpV+j(61C^xwC}=u;(u1bC!s+vzW3JXC5rw=18LKJAYGs|{q3!px0OiK
z<yd@Subn%E<DjQ^6A=nb-Y06R`Cw_$*=n?C$bMo=5T1{jOGGTREV_^%l6DK3>FIT!
zfVv}+eoJ4wE{YB_huE6KO{uj0-jd2&cw(dn2h#Yrx8|2)Y7~{p4klU+wdUf^LR3HC
zZR&~^2_2a!eJd@Sw1_M_qq;m->;dBDX;jtd%Tv_9^StW6@`J-A{1#i5mo*->{&QMJ
zUJx})ct=@*H%(*N*D2YpuqL7>wb5qs{k6}DzPGr%n9KhYA#N>3tp#5y?7Z9PuaQeE
zt!qCr7k0$NOb^}uH2m$YId_}rv*ob<vV^y_XSd{{s-AUd%#;q%cBvI3F-wtPb!ZcT
hL%iRSw-666wS2aX2rAn)5g4L=DGzmYO2hLi{11Y>uR;I-

delta 9180
zcmZuW30PIt*6ZAR&fWW74$~zN1q4(CK_+n)5pX~S6$P9pL~%kCbI1X&G#6T$))sTl
zqSDGVxsqm9PtE6h`K+gzf2B5A_A-6dE6YFMT6>=h^uG8w`>eC(z4oxy-goV-*xNtE
z`WNQgbr%4~|LWrP{t28_7w6W#RxxIM-&tuHJ(8!Tbx-b^(KR_eeON}Xv|cd@ISUq4
z%!nCMS(eht-{tRWme*1KT(q5DKc~=ZLxR>_zDu<}^ggg%%hDup*|ypqfSBBhjSIW<
zVE}!Yn0ne4yP;4IJh06%g%Q{OfKL4-cju8kbP1G~{M=RoQx~mLimojF&M7fxJzpxI
z@e#XXesk?pev&k{&LU+$6W&^4CLA#osqCaBUUW80VJbdu2$4K-H_DWr+8<9UpyXDV
zAxV|L-)H!f_kkO)c8$^jqBf-7Nb{!XT8iZKPT|^21)VarDZwP<O=_zhvrFiDthOdW
zLe)dHO4(I$eWaEtQOTpUHPQibWQI0SqV#etC{9AHYBeoJLJ@nkdD3BTZG(2Fr^K!O
zUOSK|q5f@bG0IkXlr6QB#BCa6+b7-k<`>w0QvN@&x#rAI82z8bzLQ3}m^#xI<b7<E
zEtE@%=f>O8b0l=}Y1_(<5*qim?R!hhyEdk5l$^G`Z%S(71>1awgtmNY>+cAr7$xs>
z#AF!&^b8Tfui5*Epoi>!-tJ%8hAT}EU9**Ll2YH^YY$DAko`4#j?$jzwJ+)=aYt|1
z>lAMMkM>*@-|fHH2P)|5ZM!a^gV*&;g-SN`1G*fjyDtZYUAF^V7dLO)2YAz6`W?F@
zyxI1^_<AJND?&|xen^?fbnE?;mQ`VTuF|64yY=1Ak@<7Q92}wlsF-=QeqGK-@2wd9
z3xD!fTu#voq}!>f`W&TcONQPiR^l3q^|eZ1$Y}k9QwAz`=hgF1;!32aK$Pl6U$J_F
z&b>3H>MyvYRPbDVvY+Jrz9L1tfPC~6HS>z=lX<ZB{1W{$C2+V#AFgJJxmNF~#wf2&
z4^(q#T%-PyTr*zhJ9_e6(nPNhb-R-7cSS!GByqpq)JMA|RHPe4O5Y2CMwIH*sSsm^
z8prh3#(vp%?^hj-ql#LeWE@v>eSWcVq@UE1veCGztcAZ|ysE<Rw-*hEk~sIW@q>!$
z>HWq<rTO_o#uNp)jvDI}wDldI#B(PNre^HEGls{I0qT%h{rgT_ne+^!0Cg3s&l_PP
zrh+@X>&_W_l(DRfMy;B#f4gj)Qm$<J%$T4Y_|KQd7^S%Ix-mnB;NT(0_TjP@<3~7N
zR|2g@I&#AZCnnBx^p?cBnT`Q+VS6uEI{q?4;_CnD*rEbD=u1bT3Ub}|j_ztiPfsiv
z%G?0-B#Y9$EN(+!yy12I=4hp2-@%^^R!+|kW~0^G@_S%i<)J75dU{JCu`h<Xg?~5;
z^t5t99tdhSQBz0FW+yxiTU-cjWw4FIb{8<%L6n_N$cJ4nBtPSV-S8|m&$*x;o@ela
z3xeQ94twammztNTd6|^G;)3DuGKT^e41s;5=~Ys{pLyT_hu1h9<j}yu>w-hj=z`bb
zupb<OH#i)1K_t9MDvoh@i{5WL;T`x3HOD!ep!Z2?-sN!01%HLp)clRX-#MIdK|1Vk
z!9U<EgZDXn;6(7BWcM6{^Bg{OL9cAs!Qldjj~HAe-~Ny6eazq!7v#W;<iw|>@Dhj1
zM83k{Gg9z5gD)6-$>1w-_J%FQ23JMtX%^|-(wc=if<9w#fWg-ct}^%rO^dgq*-GuA
z$hpDVi=bz1x+srf2cipMqzR*`83SWYD25US*G%{pN=%puv!2pfyqFTp`ou4Uf0-}}
zicI(puAA^Z%w=%Hgqtwegnz>i41P4>C-{$eE0#st7ebY|9LvJn!O!rEiOnq&euar9
z{6=~g!fg}A!FUrMM82HXdZ<Wk$J$MR|2N@xxWhCsHBGaj-==2QbPco|6V}3GCLDzl
z{K_-oE%NhgQ!`+>sX1UdVpB|w(HEyLTXH(noTlc|{7lV+xnkr;j)CH4JC^M9Cv1QQ
zA);!PBSiFW&&KdT>ib5RCDxDA;>EG{>~$W5?rOoBTLfQV5pFF+yNl#P(NJF#9@4_Z
ztI75rh6(H836Xxy5%)w-m$x>K%`wDx*Bm)wN)pTV<l$&(FcchM0}M0(zA=RIjggjb
zjJ<qg`0?$gxZpb&<tD&HY$xGYD!w&*8;P%hwhsXtOvctBk$qqa!lq(?sZfev8caiB
zJ4%b#&MYjxnLG1OxyxWW%1jc+Iv6dP`~E5O3@De(tF~z^nX~?s8Rw8>zR;P)c4>B_
zUkm0S%jwzZxB<3+Z0hVBm@DOyl39FDk_!M#XSg01<YILCw~!BOA#VqbLN^C0r1Yc7
zY>_ru+(~BbGbu_js3a5OVIB^G4Zq7QQGzOAKFW|242%R_a|Gb$0;rOTCa18rsm*Sb
zBF{98d07iL{4HHN&hNXW(4G`F7_I-9!cvEk^(-7QfF4aYd&o&a1KUGR3-YK3twY(>
z9<(e0lLF#sQWyv?ghf*Gf>f4+n)j!&q!yafnlz_1X--4UC9<z+O`6l1G^e%DyqGk5
z6Vupw4OJgWXG=Zg^k86G5Ojnku$0`_?(rEx=pJ+s-A8B{EGHufk*jt{*YaQmtVEZK
zwGL2?d<LvSZ8S|4&4V-wb|U!S!8zh!u$n;)gL@g=$KZa1(P)Uj)8FZIr{H3LAihl`
zn!p`{{6xXMI0h8Enc_khRwT+YSnH`YLSbkMaD#}1w=oLGaXp;C346N5NX@jmpeCF>
zG9wgydC0fgv=sE;jw-evhMaL;$Sp{6N72G-g#P0D3^u6!fMH4Qww>|Q4r7ws(MYrV
zK4S30MvP;-vPjRM1_)_@P+GCNT(K$Ohw%G&g!uqM;T&Ycc^CvALIGUBak_}1`xsZ^
zC)meNF<h6V&opPz8Ovu50v^V|YPbX@!Xxk~#>5v`MXN;`^(+{A8Mh%DV`&%&Fa~Ro
zg4-yz6u$>hk~AkKy#;xj!LaX5ItF>e5<54*V9~i7iyTYQbff10Ut_Gl0ViC;W%z9i
zuM#b<Xc!+yUo@mg!a9t(P5R&mcIRzqi({KjiyHSzGA?#>V<R(3yV}8SNR44A0~ist
zgAqh}R9|pg$dVd1SQ?VMvoue$hF@A}h;Gsl{YMQ^*&6l*cX>2pgC}MC6b!?68w^A~
zW>g5`SR&-Xi0sywwHdqz&Oe+PbCdUXpWhe+Ku@~&<L>NdRVJO!V;fX)RxzA?pv&{(
zuTg8}q&Wf7oZ?CzOAxDzS&*nb!2-P-i&(m<X5XF21}VAVGFIMA71!+!%{<``Ku;H{
zlv2gzCEOvR2Q#N<p9_*;juZT0E;SVl=5eTW;ULX-;r9XtRW6)ebEsL!;cj{_Vz8Kq
zOI#2KO9{G%nnk1vn>biT&2kPa=)ICdwI5C?j~}dt8b7!f?xO}5<O3XfKIn(z`w)Xi
zIMkBvH5}HuAR6Wq{xJrRlZtg5)^m7*!v+o;89d40DREyNE7OFyTE|Z5i;+*fk;2<~
z&u?a$EvSmYCRC5UGpIv;adiu;_U{gxP3Q_;Oz4JjsM^Z%d3Si)#P!l&P?2G7fvq^H
zFdGj<jFp1>o0uN3$%DZr3?L{Uwwbtkb|7ne6L!Kb1TxW%3D3Z82G5%C9Mq!&COi)>
znD8R(5z%&An2BtiNyQ!pdxf^c2o=YEz;dD0c2*R;1zys?5mUZ!{=676xJSIT*LIf<
zFT*S1vF$9}re%qmr|qG_^R3|!Z*FJH#krkEFH!g(N2qt-4(6wc+ShEIiXj%qAqnSr
zXB@ytNQM-IQ{}`=!|!zH()68yQx=0EX&4WDJCW8MbAtvw@v9D}Fs<fz5x9#*wn|Jo
z2)4w|2f_X-BJI!%+jhW3)h^b0L@e~iy|oXvATuIL;a4Vp5!6>&B`6Ca8}vi08?-y<
zke$(fl7s(<(<stpU6mMQK`rP0QZeoHl+Tr7jRr$9Q;FeeW-j<sW*kvsMg`5KPXjPj
z`ZNm{{)w<o6T}i8jP8>cZ4U#-o!m*Aa|5{C9zSep+s0P|nE$JGTnn{rn>v6~%2K-w
z)zV&-jytEn+&M`x?w<Y)5YPaDbr4R<6(UF?m|hRMeJ={pSa^Kp%p}}oCgVs>krves
znBFuN=~zAvMVmAN4%|uOvT;)4gf6iB$hQ126B{5nsR7)WZpeg94!0VNvKE?6pJor{
z;bBs>6Zg9jmbzk`gcPml#1jySD(~6`q3+N`yWRj{f6@uxaL;WKt!T`+G&jj(+_Q1V
z#m)`F>~EvN)ILB9l$<@kSObEowH1!R7`<;|BZO<v2(2|3p4<p+G@Q|=5Qxy=7)18g
zBkO?M`__XClQBuO)*GR%1}7omFhq~D)VX7j)EfPbb+<zZ`w)x6>xK4jCJ}!J(iMjU
z52kIJ0%If^)nM#MZO6?JZz(2Byu^eyi@FnJ96I>Sb&}?!BV?04(H=V4q$GAs{hh8!
zZuA6=SyN31Isd!hAOO~L92P?$mRG@8V5MV8)f<bc94wv|VA<rsjrc)q{{{EK4{*PX
zbXN>vIv!D}uG1k3&R{h+My~x|U@VqjbU}IpD~Sm>n89!rtArE`KV^KHUsBS8laA6l
z2~5E^4ObuFze5y*sTzaQ+YpHbt|R4VC}2=F6`wme0}Te#Ee0xoZHQ(t;}%lNQGpF+
z;-ix5Y&=NPu3^JXV-*xRoR}gW#`?fYrwm;Lx@pX+XKq7g%l2D3oDakMy)Y(H{aL~j
zJ^h~Q#GK-lrFaRlV=s$glI!fqkgS{N`AuB}mTT?2Hx95+b;rURS&q8VDLBD&O>!IG
z;N2WrvUA0~`Xq~2mn1KqVXr8j%(|1;iZGiO1*t6k_*oY1!ApWEF6ac<@lqFtb{hF#
zM$mK)GyJf-Gb!oKa$%8!sWuwsa;PBmJO-7-i|MdjCS%OPjIwYi%CrHLhl61W5tlN`
z!r?HD#E}*b%kbbzj4NC{@oOc6YLZw*%$SSIVYMHY#P|B)Ot_yKOqZC9JHkWMJd7Ec
z!J{H4NNele_&&=q^lApR;-e2)H+wp)p+jtBzjRn@Qj#%o7Cfeb-+&o+mo1#VVA1UP
zm6(xDtd`cx%*o&h6E?s`;v0Zx=^+D5ESH{=NzRG+3iG0XP3o+??*hwl*Fk{^n<+V`
z!xj^^!Zw+qgH_ta44n@<P1uEZg*!iDJ=)=xBeSmw&%$#I>SgLhcPaZ~9^Qiq7gI1^
z3cUn-P230e`m(#g19paY<wbT~^KST<MQX{>7%&ZsPuh^tF*yzYm`3T4pb}|@`1li+
zt#uVqpR(wZZpceZiBb%uQTj{8U8*zk6GYl*lTXFXv@?!;B!uAdOTl&12eFjh6ebNZ
zWFZr|GsOB&S&XMEGPtC04vt_h)-OI&fla0YG0!SfftY9eN$x;tp0ao#R=+tdOest*
zVpMfN2@c1GOd|JobdQ#EQeu)@^MXjb#1gTa6E3lc*<?FWQJZWhHFYxyYbV+rP*z&B
z%g(7hM6|RfS}xj9wg;g$%7w~yJ!UZSxUaZ$i6wie?g+%>XW;Rul?|x)&@s%uQ&~Pv
z{{ozX!!b*Yz>pQn*u*FeP5$+j!KY#9D{CTKQ^*yDyc!}k+kzu3uZE(Xd@v|AW{CGM
zvjh*CKMdiR_FLob+ok~`+>zKM9Rl3wBO0JBWqrH!O`UOya8oMAQ&|Zv$kEa-6^Fi-
zUmS5X0kkG>6lNG=Flos&ild=LpjMn#9;n9hAli4ZiXMhh3G9qd1H`BT!Dxh7Ed4N8
z64*{hFbZ8Gw4+SeUS&c|T6K_tnJ|vBSI6Eu<(7DY14xv<5{TX3hFL5|nybI_SADNX
z28cr65pytLLSUE@oR|&*Fd3v{2FSp@e>6<R)KiM-W_r^!9gUS@AzqN^ICXo`ji4N!
z>ZakTmI;TBdh;=V^uWRJtq3JK4kd?BjdK?`@bnkYV7zu40?>T7Uy)fu7vwOZQ_a;K
z21b=(<gqGUW=W4|rBN}V)~HHkbp167u`Z-_#I13p<A2U+71uIdLt3FAJ$==6^W$H!
zyS%+VX9?;meEJuxO8$D~z3?+z5hd@vM~Ctrin=b0UsG4u)e-z)J3Id1D7t0wo=rbF
zip5!6UZ9KpSv*x<seh5hvm_ALj}MYSWj~%Tfg}C+L<vM>^D+t4Wb^qF_#vB*mq1|-
zpDck_b1dedTwWnDo?O0&(=Swq3txIiOdi0)L~wsTPSWP}=L;q9S%1Dr0^<f)z(0II
z-ax)glHM6;k$Ml}b0nsI5T7l9kUTy?0#!cXj1Nd2Y>{exz&Ac1Z;0i_Geaz=Z9}d8
zOc`oPy)l%_pO=K0Z}o6qJ};5Bj_31I33Mvp@}~!}zJSk^nBNMlNR<w=TzzjCUn5DA
zhVx1Zyf@rp?m2?blbGj6@D&p1Sjgu}U}GVlCV^Xp{2mD`8p)SS;O0nc49Z4X%x6bg
znsbY+Ks6Rw@rf(u3#8PhVqPtQ@DhvpkrGSKZzUE_<!B4IGTI^)jj@2^KA^`~3-f{x
zh!|&K*7|@uKA>v6W%TBFtEZ(CtbiYzU`chEXpweJw484}iLX>XPvT1@;GS#+VeMqT
zN@4=0SP@$@h2JkRAycgx_3%`FpW-RCB34^!VS=ae8cBL`nk5xkW{u9CGRtV<bpE*H
zIWnDBNg!>8rRSv?mKzD>))W`zmOtS$t)6b0$sd$bv9l}_&(GqIN=&!e7U`%D$eUwf
z{xQeu&hWX`z`Z`#vem7^(tNPO>P4S<yjChaHIHwWKzXIruWOaolo&goFOj6P^DXg_
z3;0lp*|xxnYIqf&DlsdntmW`wm9+}GF0_F43;9^d^RI>0q#b=Xua<Rc^KWC~%H0-w
z)*>EZJKarOS;{*I4}M75t%Utxkiy2S#0#bCi?}<6wuW;{Lc&*L6+jOioPB@0Yi18q
z{M(1KFmY@#mp`tG*^5zCzfp=L@1|Z~%;oQQ;tY|FPasmFIJVspAOa^bhe%vviS}B8
z^nhuKzIut}KyJ%>E1z|I@2*)Yh&6?-v6QdgHb+k%LqF+Jm6zh*U9<LC#hSg8w~{>`
zzZ7lldXccHz7v5`(tH*GOb*R|yKCJ0iG6?!%jG-wEVzjWEqbUH^8M|u8RI3cM6n><
z!Nl`Jt-jaZgZ7^O3z0gAeR0ebO=0<tNV|?JQp_jz0Fk-Ok{Y=TNw@y4NS~a+ae1Ve
zo6>>i1IGW3%bqieACDYrTqHlHuI9|;^A_K`Yl<&h{Ful@#d01Z`HS9o?7iR+yza$k
z;2-!;TxsHu5|@`-v9G;gE{=-=poj9d?{9Za@1L6ZLqywOaKuNfutt3H3Y>t4++4(#
z;jf1`!Z{P`Lh(*=uaDs{G5kBkVz?a5+la80R&bJ5BJEPRMcWs_{lwChJjn56A3U4E
Fe*wc|#SH)e

diff --git a/settings/repository/org.broadinstitute/variant-1.85.1357.xml b/settings/repository/org.broadinstitute/variant-1.88.1401.xml
similarity index 71%
rename from settings/repository/org.broadinstitute/variant-1.85.1357.xml
rename to settings/repository/org.broadinstitute/variant-1.88.1401.xml
index f6d7a2caa..5db78b1e4 100644
--- a/settings/repository/org.broadinstitute/variant-1.85.1357.xml
+++ b/settings/repository/org.broadinstitute/variant-1.88.1401.xml
@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broadinstitute" module="variant" revision="1.85.1357" status="integration" />
+    <info organisation="org.broadinstitute" module="variant" revision="1.88.1401" status="integration" />
 </ivy-module>