From 449bf1b539369011b5d2f5fc946662686a9e7c30 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 18 Jul 2011 10:47:03 -0400 Subject: [PATCH] Testdata for diffObjects. PipelineTest updated to point to MD5DB.java --- .../sting/queue/pipeline/PipelineTest.scala | 3 ++- public/testdata/exampleBAM.simple.bai | Bin 0 -> 232 bytes public/testdata/exampleBAM.simple.bam | Bin 0 -> 3595 bytes 3 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 public/testdata/exampleBAM.simple.bai create mode 100644 public/testdata/exampleBAM.simple.bam diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala index dc3cfd9d4..c2c956118 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/PipelineTest.scala @@ -31,6 +31,7 @@ import org.broadinstitute.sting.commandline.CommandLineProgram import java.util.Date import java.text.SimpleDateFormat import org.broadinstitute.sting.BaseTest +import org.broadinstitute.sting.MD5DB import org.broadinstitute.sting.queue.QCommandLine import org.broadinstitute.sting.queue.util.{Logging, ProcessController} import java.io.{FileNotFoundException, File} @@ -105,7 +106,7 @@ object PipelineTest extends BaseTest with Logging { private def assertMatchingMD5s(name: String, fileMD5s: Traversable[(File, String)], parameterize: Boolean) { var failed = 0 for ((file, expectedMD5) <- fileMD5s) { - val calculatedMD5 = BaseTest.testFileMD5(name, file, expectedMD5, parameterize) + val calculatedMD5 = MD5DB.testFileMD5(name, file, expectedMD5, parameterize) if (!parameterize && expectedMD5 != "" && expectedMD5 != calculatedMD5) failed += 1 } diff --git a/public/testdata/exampleBAM.simple.bai b/public/testdata/exampleBAM.simple.bai new file mode 100644 index 0000000000000000000000000000000000000000..2d8268b1d9ecd4c5da64f692d7790723d89e2445 GIT binary patch literal 232 zcmZ>A^kigYU|?VaVoxCk1`u108At$u6g!0Wf{MfV54a)X-cWHEf0Y14+y^QS<8z2Z r#QmV+Fn*FO)ci>d3`{^K%wCwdB19Tag4_sGgYFiXT`(GE2TU^nq8kf) literal 0 HcmV?d00001 diff --git a/public/testdata/exampleBAM.simple.bam b/public/testdata/exampleBAM.simple.bam new file mode 100644 index 0000000000000000000000000000000000000000..c3eb7ae7bf90a4f4aee3ce11cb0a3bd63139d36f GIT binary patch literal 3595 zcmV+m4)pOKiwFb&00000{{{d;LjnNq4Xv2lZzS1W$J@~Ed%Jy3ovJ!@IamBpFSfgV zccY-KN=aKAW;V-OpnyP&J>!9uX2!GjED(`^swjn0ka&SdlprNilm~<&B%XQNB@aC0 zA@5Nn6eOhl1&HN$s=Mv+PJ5VQ0rzq0zPjmBG9+Wnn(r<1L5 z_wBDvpI$sY@1A^h`rzW?^5KV1PoJOn-a7fM?#a8;2Y-Ay>E44A$7busC)4ch$x-*W z-=A(@oqx1_dH(49^8D$8^Q-Ob;>pDaSEtWDJb!xi!Rgi2`IEE9U!NRp|H=5SLtBqd zub!WF@9$5K&(9tlJbZM#cYJU#*?qKoxO;xMyL)`_aQ|%g?BML6d-C4YTtv<<(tGRu zx4ZA8)AK(&ee&$_c@p2>Iy-&Ry_bA`<>db7R(fx}SO0Qs=*L@!Ta(S>?w9Y)Xs#|E zJ^$0w%k%ALA3iv}e7ODK<4b^hzP)?-@PlWkm(Rbx{p9o`v&$!^&*Ww*H?QPaZl21? z{uutA%N@8)vcA;(3cKU?-up@%f9-4AU!H7E_IEzm8IO-Q$CJ&S{rShe&GF&(Wc%de zF&Mgee6%yU`Oy}*XY1nQ=UbyvhfaHX*_7$o3H&Z?0@muXP;ePZhSnR z?Ceh`)4iSP{$yu5Ihq{)+PLv=%|-+3{N|<1JHh51nU#W~B1XBw3N|e?mr`k^0voeX z3D#3|Kzkje+w_MR`qE^ThmN<}MONNrN zRpv`B`(l+zzAilgCgCb&&Z^fJGUz%Zp+f47m=MSh@!c$qm4#p4xn?nIW_y|CU_6~n z#>W73+b>AX9FgNF#!+6V*l-jvMkw2W#V`y5%d?$!$OKcIDHZyj=Q<&$Lh-QO?y_}Z zE3f0WT+(cY{a$wZIwbo$0J#4o|Xh2(cvwSC7uzc^D<(IH_zSJ)VhttEo zz3F6kvNLB%5v?#vkwRsO5{y)pr&WazRb&I@5MMFLQqu9jO>n;<(zMb%9E4hj0-OO~ zL-?#cS%)D+o&s0ZXK6TS&Vx^|E5ulUkdo?dmS0}8oLsYf=M7k*GO7s1Wu<^6MzJnq z6cuHKB8rlN#oY6dk&;y^P9J7E0DySW!q<}vVW+Diw`68qeBcY8;q}zhLVu6Es7=(Ra zvVbG(O2$JwWXKWWlGOk71+!-;H>v;4*GKt(7*w2;RAXsd3}K>tkJu<++~>Zdgw!cW1cq2>mEXy-Za*T=2W3AJuP#YU*RpN~#i7-?K(q$IytajRt43R{R zJ!*%eHkjSDZPY`))9R1f6kCwsc#V$w#Fm|o61;zRkga{Z2(lZ`dE7gck@^YbJc-JfKs>1e5+NyxjtGrooRAWDVx=P`Ak=5|NSb^%HH$)mxND|` zb{wgENF~i+Q|1KDd?lIiIHQU(%pu%VphDHM2jXs&FI}VD_+{<&QR0%INM%Wxlo;!h zrb<_skXVz7BxR{lq)QyxULa-Y^t=w|E+;%Bp%fvPHkFns1iURQ0ewbF$(8H)9MS~P zY|gl2z!dS}kP3oVR^(1)D)MjM^2!0M{q^#$Z&3CRpi>?#BCNo9RTd;g8O~{rpf`d? z$^u-0bXgHpCV52_+}hd~VD^aDrA$c+-r%L7cPhB?6fl%wF(xx}f)t#G$`y<==`f*u zr|n_;ZkB^W(2UDu-fY(J_v7R&{C+K7F;oU4}|GZ$i=`P=gwX5YJc0AoXFrD&X z(J6_pbWv5nlSffe6{M^nV(p#s4Uw-)M@ zgusW!s5qZ9KqSeTu7QYB!eBBJcdYKHW)o^IVT`IV+cLi_N^h%H@}Dymefu_`Gor{voX|3bTxZnwynw9-WZkiC+H%(eAGClK1fI+8hB1b#;q8QJz6s27 zkn#l(lqj+~9IZDy>)k=iwcOUg5-ti{F9bbLn|A2cffa;Zw>1ha=!rInmI3F1<*)Nj zAUw(fi-~n+8JTl;QU2+Fn4)~|mS=teYu{U*{m0XZiL&vvUuc!(#$eFKR8>etIZkK} zDFj&)p{%4uRAjSUQQWk^S(ds&dSrK47piJ1*7hF1!MYiw|3A~_> z7=J~7`NcKLjbDEH`Y5j?sEog=q*4P&0S}6*YjR#_OHt4DOxD2IC6LEvq zDKQGnKu~knIU_X`IK3oa7AW8S*~?z}39S9q^4#B>9`B5&M@PF06cr^1Bz_emmEnq3 zMNvT7gV=Lvqyhfo<34|+NjGDvj+bEN=1V%oe1oe}Oegq3NHfyo)j z_;4N0_G^cLFO_tRyBMk~+AAvZxBtsj$zqG7y-#E||?npuR$o!%~`uXEJDl zDu8rXHq6DYa1EmL34%lZ2-8ry6k-kp=-n{W-(LZkcW-&-A7Jfdc}X_;Z|3CvYY_vY zm}F4SXjUdFjZ!ECxQJq1(6|J5Y*ZaA;$<>9@UsGZ-@3YI#uL)(8sPegG2=9t?;G-5~U&Z}Yad zHe3(EVK1Y6GB^A0KU!(<#%-_s`sGSv?XFpDA4aj`#S!<7%?k=@XroM(2tfW z{!d=8nmf0hV(4Cv1iD}beLt=eL@|Q;ML{YTxI!@ulLbw2oJNV7OAuARU#k@;Q}w#y zb}d)x2}Rb!a(zPmbjHm8<`AF%^c7m{U;ca%UN=7Jd}F2Yhs#NhrboL6)4jb#c*T$( z5ynQ95pl!ZHwq*^J~ zf>$nFG*eu&qqTw*MtSPl4`#k}XEUXc^|zN%{tsc(yPIMi001A02m}BC000301^_}s R0stET0{{R300000006Of@cRG& literal 0 HcmV?d00001