From c0b61a27010aa565be14cb3769ef78f21f857678 Mon Sep 17 00:00:00 2001 From: Chris Norman Date: Wed, 8 Dec 2021 13:18:04 -0500 Subject: [PATCH] Upgrade to samtools 1.14. (#1583) * Upgrade to samtools 1.14. * Update old CRAM files that samtools no longer accepts. --- scripts/install-samtools.sh | 6 +++--- .../java/htsjdk/utils/SamtoolsTestUtils.java | 2 +- .../samtools/cram/cramQueryWithBAI.cram | Bin 8947 -> 5429 bytes .../samtools/cram/cramQueryWithBAI.cram.bai | Bin 152 -> 152 bytes 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/install-samtools.sh b/scripts/install-samtools.sh index 671270ac93..84feb30700 100755 --- a/scripts/install-samtools.sh +++ b/scripts/install-samtools.sh @@ -1,5 +1,5 @@ #!/bin/sh set -ex -wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 -tar -xjvf samtools-1.10.tar.bz2 -cd samtools-1.10 && ./configure --prefix=/usr && make && sudo make install +wget https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2 +tar -xjvf samtools-1.14.tar.bz2 +cd samtools-1.14 && ./configure --prefix=/usr && make && sudo make install diff --git a/src/test/java/htsjdk/utils/SamtoolsTestUtils.java b/src/test/java/htsjdk/utils/SamtoolsTestUtils.java index 4755665f93..f70674d8cd 100644 --- a/src/test/java/htsjdk/utils/SamtoolsTestUtils.java +++ b/src/test/java/htsjdk/utils/SamtoolsTestUtils.java @@ -13,7 +13,7 @@ */ public class SamtoolsTestUtils { private static final String SAMTOOLS_BINARY_ENV_VARIABLE = "HTSJDK_SAMTOOLS_BIN"; - public final static String expectedSamtoolsVersion = "1.10"; + public final static String expectedSamtoolsVersion = "1.14"; /** * @return true if samtools is available, otherwise false diff --git a/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram b/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram index 77a5ef2547e8ee37615dfc67a5a0e3dfe9d69158..42c8acafbf24782547767b1fab4e50b0183a44b8 100644 GIT binary patch delta 4216 zcmb_Ac|4R|+xI=WJUskonm5cJVAVppe~)P(2P zg+r`OJq13>IhmL3?DBcq*F>d!&x}%Ehu*>t(5uJBi!XL$^e@ERLLRurz(d%84&y4^C!F z3l;~fT$Q@oH;8XC*<_|~Y*rTk@${~Em^%z{S1?&Cnjw$#=o>08CI?L)@wF5^E}(Cy zy_lRfee_C8@%%6>V!@H~UiZi;fs%Mk8gv_gzINJ&Hvx~Ex z3(L8EIv6HXe!ratQgrP0iWPiqN8(j{dF{G{4%tlyl><%xIwplX7j|=Z%z$3tM~giz zdkx~axBX_n=k{y5eH?wl`k@wm^6KD&>lRvuy&l(gcQ9Wo&G;FMob&wgO;;fU&d9uN z-c;5xe)vjmU`oiTsGSEKMJ%M~ZH3M`cFggks*K{U}wJKhnU>Z*VL(CaN7J7j5>-}cM97M$AiFqB+cR=(%6 zf`9RL(_~rCe{{phPMT{QA64wR*fxl|w4o{Xe&~M9l@II#bSBpfi&LiOAD<5^`k?7B z71@XDaNm-)o%t>?>&A|{K%WZ+#gC=u!aH74d4IFv$XB&PLWKx<{Zq^g^>o{+jD-8OfrsHSJ__{m-oogUOb|%UmMWeP;PcQq3)T= zSE)<3&+L@P=F3u59`oLJ)$?rDc^EZ&nEy4Kws!5YRX*FMm^Y;!r1)%`(^9C|QkgrO zP>|3vQ@HkIL8G?cC8+{pX_UvNn7$ZXc0QReDtBDz#*2HQUV+$0vl>Sy3;Yuv~LAj+6 z8hXXCFLKYS{OnHpOp(P0($O6Or|#g2JR7LmW^G-%;WEn7Jppwd2aYogjkk+aw$^;m zG<4g(EK}x;kukcg;PvVkw()t5agAjKI>T=qrWD_nR;zf`I;%ghGfPIH_j0$9>0VO* zR8Hxr_VkO~S0m!Z_eo|hYI&+wL6Nt+Op3=S=|9$<+3S_4Ht{rJ>u})Nk)q^$Tl?Z_ z=UaE?D;g}dDm-mQsTY0|N z@4>S9)R#MlsKhu9XYJkX<1^OWrK^Vf(l&T>nVnCwc{;e}lhPDp%6s6YCbm0Hsqc)O z=22tsP%~(oliYoYPja?>v!|MJ555{D7}^djlRmbbZXgCd@i1aOlWEn~zjIafVOl9C zb7kvYbig7hQjC{WGBOle$*}6%u7y-VIphnlOIOKwAUi9WW`rU61KD=GwTy4;c zdczy%^vT%-K6RxSIa@nrA31V7T1u3f6k%~=HmSh&ijC-`@;B5E^?MhqWO({3wNL1% z#akz6`rp^p`+_^o%u8`JSvGKh6BCDR}+!a5^y=}GEd&9}pG3_ILt-Pglv&_@f`!O9hsQA3NunM1JVHybzq7vdN z3Kgl8^XXdBPAa>v9WJUw(G*8T$i_?CD-M-unz*$b9&JrY_Equ?-La#0_SxI;xY#0I zYJ?hkW>skf-EF~sM-8*^$Niq^yti$UH@|h{9Gbmyp;~nNGr`66-_dhVpILOv zLeSwa`wv)1{I^;CfFJ_ItI~xzF1k*qX82Xo^-P##3&SYaEijCBb%bHW(iw&^u4EV% zaiwBVqF5>r<0t@$Qr%z}PX%Hz8lVU?pe;@#!LS643d52V7Z{eZ1(dWcP+4LN1Tt2Z zFf8u^lohN1B5n~nRI~1W^@dYZz9w1Nv%wX_)i-6^ue77!fQ^6fZ^)mync_ULqr}KvYyxR#8>!v!u}btX#bMDAoX6=zUbcI|1Ge zytf(vFa$sXKn5Tja{@rK6uSR!|NggM3tvntLn}I%H>lGzZ^AdsLEOmw;ir@S#LSy- zu%d4Nhs?^@ioO}xHFMt?ANo{LJw;pT+#bQgwrdPx#60D?xYGqoUxj~YBDb`f`y_rY z5paoZ$%n@E>6M1nWXpZ*d=sO63oAOA7H_3y$a%p+#_eDF%1Cn%BX&U_ z!T^Cjc5wafWm|5Jcz{u94kWrQH03N1|YhSVjbpeNl$vq=WNO2 z9fx>s$pU%`*kwXdIt3s;51>3&vVaGMq5NGcfleQADqA<-(^&Up2#?H397Yh7HUU-! zQi3of8t9{i2tpBA5Q-^8|AIg9$vXr=YiK|UKv6@e&1DJFm{61pLGKrwXnRkP*?bAO zMgDXf3_J!4(f@e+<@LgKh9iPtHZFnI0f$S3UX#pWnEjkJ;KmwYCb0%ivIYuR1CLn) z!>j=T`#E%|@gbgW&x6*5)3Eb~21uuC?IQ}sOdEX|5SQdA!97-(QSZWOjZIbl@GmGi>fj3_ zVmeBESdnN~#f=DKr@#oLl`l(F0;Ui8Ij<3f;I9CC0#3L-U>D?gv$NUk>{NF4C3ZIC z%}y2wK*enDBZb*u22!C60pCt>sl}q0#+n)XWC&&!k|rG&LN9I8qvgVgxayw;Fc^W1 z;Gh5mhE6WNUN5X5`?cJ47?BW`jJ*^5AOc1tf71RLFK1yyieF7s!tPL>w}%mF{sBc5 zW|*IUI*cqKv!nl*m%u;-X4uLbh@%{(mYOK6L@mJ-1_ULQ_~ZTev5i(6L~!f1OBxFL z&1`LbT+?a-byv4Q?P@~{(J(j?hU>IoL}uxq4pUQz80*B%1}=p-UAzdiMO<;0P<1gW zjd>P9vMh-cN9M#)S>rUW3`DX_i6C*3sH}fzJY$G# znM@{eM#vmJDm#|O(SxX#QY0xdj+)U-!$CAlZUl*~O-`(!vX0XdwIN87OW6@!XopJ) zhNZ4wUxBRNJAk&=Iz)=qa`E3Ua88wU+ru3|w7t9<}mXq38?E@PRY(@#;<@9*EGwQ_c zk_e_2-QQ$TJ>PemE@~$!vT{}J?jUyWIclB5*WvvauRO0`Vl_>`sVwet3Bd;rq3z-& zuix6mI8l6DD~oVEeAE7_<@JB3C&UbYah|9sms^$=HmB3MH9qLc(<9|FgT4_po=Y|A z8O;89dByCGcP~vbB@MA5OVa5>!4qvBMupxsiSMa~K`=tx!jAgA#vd~ui$jLE+WzrP z)21IwbyaZ4@_uQnwBlu(@jJFZzkzygxNlD(@BH$DzweC;Vh@~Q-pr4gMo-Ya1ERpv zrPW=Cf)Pbo=$A)+jsgMev44*ej41uwaA8)N;V_~sqL;70Ms+*Q7lbg$xL& zUR8$!6|8T~ZKbl7j#btk=}`(9MKqJpw!^5JVQvw+YNPb|)b$AA@LN+BDb zxF*m64N-%g^;;<>Di`ga%T<+-sI8ZWRLgd>Wr1Sb2S1bf=E|#ehu;){Gep=v6)?Yz zN^ij^NOEytr?6iv^bCmu6)N9FRfU;zVPY6Cpv|(Xd3C=nJ~}txYYhlv52sB+bWFqo z?%aC$c|;&+8Du1@;+KtkVFGRL<~=E!%{$>G78N^j^}EfOTaV_c)f>*Xd#CuFj-6;5 zjI*gX4O0{B-pQ;?IF>)h&U>;l2ZxJEIp)3>?aqKp3{P=voux5S&Jv-TO_V!nUivli zk}q583}!di=niXNpX-rcBcY*5epP!@50@1Xw@zP-!Y0+dXc=z%a;dlTZGL?8+>?7N zz?sozr(Op(KFpS|;J2!%Bf*f;YW^f3HhwIh=1Z!ougDGk)Bwr^w+98>?;=ZSNf3k! znK+IE(=w&gX2sW2RY%eTQr7b+su~EkhCIoS03+CP{0zTbS$$PT-_Bx5pewv_NcPz{ Z*#a8;Yk;ZlZ~`w85g1??nxMlD{{g^jsyP4v literal 8947 zcmeHMdw5gFm7lq~k|n>v2HVIs@&hn6$d+V-W1_8P$(D^}+13MG0+r>fD_OCuD0)TjZ8dUKOhCTi7HJ6*2c9#A4`HII>1s`hqSdAYn?4g$K`Y9r@jw_8`s zsw%1!B4cy4UL})Pt*sKN_0_eFi8b*G&G;cvIEx=nS9mjiNEFWE zhtn0_j2{w(v-sh3gl78r?S5Wnir?r^C&9$KtJgb>&*cYDbk^Rw0+! zL~31ix0~DMR=HfPi}fk*C^2xhTBjSLutVau_OQx$w#3KvdKp$(*45kNVBKX7pLKPY zXCmB}kwwdFR=>4O&GmS!kP0}ruWSRX4@A~hX6rQSTcP#2Jrwr_t1oySxUEsjNvWg=2stv{-u`y*~fMo-94A*TLE>9;b`*%LrIN3qfTH=N5^sMPusnvc4|P zWvl1BYA}Wy?4zudmP?okBWPGZ>m{ku@8sOg9IT`?8|y5FI+eyKVcmW&=jor+qAZun zDkVME?ch*0U!%L3?cu!rN?9dI&4k|QbM9bat!A!|?Sa`!#W#Pk!)6EJ}zlTTxf`*duTSZyG2b1hz{1GeIdITPWStPY>jZgu%s ziF>29zopl&boaVk5^!AB3;t*sr&@Y!l@o$Y7t3^8SgY67KQWbS)q3;FzDSfAg?%)y7tFgqu)ChiiOteq~_z%t+?od6r`IM+qC zv36^(i@1r^W^s7AUe6eg3A)E+_1igb&lnYY4ErV7G3s>5ZLmphn}r;&#l6+1tdu~l z$9XtcKRBYr-DzdIm1`yJc82v3cowJK;^r)Vu*ta9d>ljoSPJ%F=>a!W8tY7!Hp`|u zLkrv(!gF)Lb6I?Taxjj5rK!Qtve8o4uC8k}HMZy_V{`39WqjZqyp3B;Je{dvNc`=3!MSs}QDtSh#K!44|3)u_i3ulc1Ca?A z0b6(+7XPFV*{x2OWt-FAMXbbfc1w@d+s%3>Y}M`bnA^-A5;4a~YOW7rDU2aJlgptc zM>|PeB_WFe9wR{>M^^VUuK2OW>F#AF`CB9tUe>t{N@aaDc|k>9F0GW_w%RLOlSs<- zTc2ANxMhJ`7Pw`BzY7ce8Gd;|$M1T~o`6CpSL0AK{3sKu57h^b@eO*cYQ+WvHa0WN zenxE41pXDZv~6lvGf36UG;20Bw=w!=21p>$Ue2`3n077G4*eFU-J~KywQZYjLT;uq z^_TR`u55-};QP6?^%x^Sk8wRTRJ|HwUYikPTBF05U#r4cVA5lppa(gj0cawF7URU` zHjI-DdOjse*2BCM6HH012f?&j=%qIj&H@uCTi6T}GxR{rR6}o(2~=bo8Zpi>0Bwm; z4T9nZ5X^1WV4N5D-_%jC2A#~K0TRMA8I6K*VibFf0;5sb9-l8FuTijVoH&d|!8&mi z7>$DE;}pPX6b>Rz21cWBE^!nXjlwa-Q)EC&Xy$LnbUib)ku z0T-Z<*E{ZBrQbl9;?aCTf>4y0l$?^9mcC$NM&=^23$o*EVvii6V~IF7FJ>UJN3!$r zeGudX8NotUC%9w3B{oX7CUQT#{-Za)Q(bWGsaIY^d~j--M&=Z(gI)@`sm2Hj3`WBd zgw%n1qo|HF#yV&M!3YWuM)w0J3=)yu2t|;3FlvO({s;)5!rhogtFSQnBBBKd3uzh` zC7>msG=XT|Q;c!s{!k-2W=-cMoRtWkE!vIm&wUBJjnV|YOYasEDflp*oiw)BFRst- z=5WA4iQTIUEt9X*#qZbP@|GgigYPsBlygLB$cY9QH<0_x@LYdQmzO zX2713gwUjA4MxSV%Y_+((Oh_E@G}R@iwDeEXuyo1n>S!CgkJ7oR03RTFq#LiT$q?W z7%hbE65!+^=!lb(LP#7!xpX)hLSug@EofdCG-sfoc~Q{37+y<)W-%3^Lc>AxI8z)n z=VC%B44RjPhL?j7S`=1fhZRf1isGn~cg@Gprz7f_$3eeK!1u*#d}w)51wlJ`NhJ2c;e1Pd?PyL!G8@I#R3l45>qfricb4e#_U|P5c zPl03*y64Z-Ir0wznidr&U@`P!w~Yn=V@ZRMFfjShk^l%Melr2DnGmERh>oDd!6>3= z5U1(EXd?J(B2ZG`okED@Lm?V2M+w3??U=@NQnp|U#?wbJWkx^#Py>jKsg&$xvl$myPYy;`)pl1r)M|)4FAXze%bG>Xw z@Q;dR^y!9N!Qq#dpqxj}Ji6nk7dBl-e_}RUJ+XMSV6J0a zI2R)$hd;G4W3$;h;6Fj%MT$yNTiQ_+isubip4oZiy=`08zkcq<{qldg z)_0*kd*lGhDBSZc6DxnLu>9qwL(6koPu}%b^Yyk}|M&XAGaITu?mPd5@!&IpBX_LK zVfM<>Q;tg>s`<}l`wD_Pi!Sp%Ia#yi{s-3gT{gV^RYl%`!?-H*AWi4QmWJ$`73V-nDSV8+aELdKdC!u$&Q`38 z^QzT*kBd-E@`-oynsz=L`0O{{mC8u#ovj<14<#|Bi;A0%9e(LAJCF9hbmO*_ool7MxfrBih`+i1Gnw=9X zM<+^6Fxm7EaSxhC6+&DJJt1M%MM$YR0EskKWd;TyIt`Fg6Y(m*uo6T?OA$r-P)Qc> zW0#YtL3>9qf^hcQwFRW? zP=D`lOhRPR!i2l*2<>|HHk{c}Lsge%Bs{T6OFc*r4L#~FI^F%zR}}?|sVT>0I>1*K zzNI3yEvX9lu?@y7H+xkumNpXSO)Zf1XSX9{d~xCwfTll;pc6U?jjpaM8zjGmVmf8c zswFiKqf8g7{EXVZ;Y{9%;t&?|2;rq7<)+I5)YCg~1yLatpdaRxK%l>?6fzal+@n z&J}F_6~2ADpdpZX5E5B@?1kt_p^|fwRb!VcmYU|yJ#!iBugD>A%j0nvHwY;7^k)29 bf`j}}5{nw6buIPKCkKm>KmcFf;qU(eGDOo_ diff --git a/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai b/src/test/resources/htsjdk/samtools/cram/cramQueryWithBAI.cram.bai index c44b7e98c4a35d21c480d2971d91f1c1a7f0dd61..b030c144ab81853196a228c5b00254cc809cc185 100644 GIT binary patch literal 152 zcmZ>A^kigWU|;}Ye<212Mj*|=u!{{uGD2yuNf7x!kRl*}(O^YDK8$7u%aTe!?1JfH Gg)#sw5(NA^kigWU|;}Ye<212Mj*|=uv!pAGD2yuNf3EokRl*}(d-Z|oJ8ltCGavJcA+Z) E03)RY^8f$<