From ddeef3fbc2f884d8ad1af95adc164ca8e5bc15c3 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 31 Oct 2018 09:56:24 +0100 Subject: [PATCH] Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. --- lib/galaxy/datatypes/binary.py | 2 +- lib/galaxy/datatypes/test/1.qname_sorted.bam | Bin 0 -> 4336 bytes 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 lib/galaxy/datatypes/test/1.qname_sorted.bam diff --git a/lib/galaxy/datatypes/binary.py b/lib/galaxy/datatypes/binary.py index 7472108fb17..a116c3cc71c 100644 --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -556,7 +556,7 @@ class BamQuerynameSorted(BamInputSorted): file_ext = "qname_sorted.bam" def sniff(self, file_name): - return super(BamQuerynameSorted, self).sniff(file_name) and not self.dataset_content_needs_grooming(file_name) + return BamNative().sniff(file_name) and not self.dataset_content_needs_grooming(file_name) def dataset_content_needs_grooming(self, file_name): """ diff --git a/lib/galaxy/datatypes/test/1.qname_sorted.bam b/lib/galaxy/datatypes/test/1.qname_sorted.bam new file mode 100644 index 0000000000000000000000000000000000000000..184c9f8db275897ced831dfc602bcd827b3a1e87 GIT binary patch literal 4336 zcmV--q99&8RKeoE-JRXp z-5|6Eu~nN$jY=YgBsPI~NNNK9CxSOE-V~)Eh@iz*$)rBVbNL@P2QK9|0saN<)+ai-(VDLrRLp zt>ulClj}7Z@>UtnN+woHON*?PN@E!$={PG)tk9ztjFHL`R*yt!x#1mLMGLE@CO~)w z5&}KBG;VkWLq<3$(?00PijssxWHB>(@}d4S>1 zD!z$wJ_MHnYAn1ntaM`A@l}CHndKmwwzTqL#A39hO^3t);MG{ zVrJz;R@IXmv8=jHS_nf7j8wml9(_L?Z0qi0HNT33oeYJzZ1wHJ^;S^TqH`=a zIOgc;K|!Okb=1OMgw0392KPN8;BI=3-avdp~>!BHUx8y_}_x0-FL2wk&+g?&9L z)o$hsvw^uIV!fSh>dp?-E*z*iYuOjGp=)IM;I{U*3i;qvGuKvFwk_nsE~@Ty4mV$H zSouv!hrj3+U>s$* zalZ776AYi7hHlVqd0wVVSfq6 ziwE1kbauh9LkFj?bqddThv2JIdm}r7XMX;3vJotNIel)jaVyRjEPdXIZVt9z|GM7@ z9?smg9)%e=cd)H}9=hMlVH2>pL~zILy=b`r-(7jJ*H{);2OiyN%PEcx?Ekl0fbHv_ zUn)IY0&hRtfqel?E(*N#K8&lYO9BsnRI06mtyfF6ldx}z!WdwH>OHYaP@JfCkn2fWXiFy&hT~~R-R*m z2zYCaQG59D)`^lJ!R2ol-VXkmP1SKz!%aU-!2c`AT=dlq001A02m}BC000301^_}s z0swFfm04YgBv%!#p50B>Jh)ReHQUvHRdsLOs=9+9Gu_iOJ!BlUb zq<6Naf2z;??D@{mcfND?Z{aA#+Ha^d{%yR^ z;k*RX>%gkwBsaLlbZ(_G&Bk$RMp3)~{Z)r^pDr)-@C@V{z5-di$u-=<;v))x9&(>P zt(D)UyD$V!-{Znvb$SRG_dUeSqtH?G$ih9rfq!Rn5&rjq|K>iu7x@2PVcmRtX=%A} zslB8fG(KC|z5v^IXYh|k>w}>tVB19iGNoibj&mt9lPRVQ;8)zpBFQr;Q>kK>t2m3z zSn&#ZNHBn=xTKuitr7gn{&I&O#IuKeUxSc-u7VL)~57U2jzDT6Wu^diGaP~==l@OLTGI}5;{ z*O2KC_UXL<|Gx_84*^s!z#klfe;Kx?XEMF9v9q<_FVL$fHhGpx(^Q78BBeN93?oY- z6QSU`vV<9lj0q;BN|>JP*0LRjYtyTM5lk&57$MO6qRKAwW-rEOEoJt(a~$-P`g!y( zAEKY8o+9$qnbg&@ZR>y{+z)EOspyZijX*L2ULKl zwZP;KHL(W9yR+Qa(Z5k4{nNjvxu10TUts&`BI>$oe&fbOikM-)&`>mfycmbHVClo3x|Wq@h!mx zBE;G*V{NnBwp|XQWG$!TFhV-onjl^JkSc$Fiu8jTD!t&dX`TuF^Rsy_krJB|s~;Py zCBOnPi*{Yt@yhX4q}O4r!)&|w%w3!ET=fCSohDe|Q=WrBgb0-DufdK9CqrKLJg9(3 zvFIC*eiw0=Ve}&+K#X3HT*c_WuFyXD_9OxajjhV|B5Y61h&SmzBG$>v@_fuX)m7CwAVhdq+M+gKMBDhG7`?y)Jjt(gfe0)TQN#|9P?e%=}f4o7*dW^+@g$oy5+KVvrWb9dR|zLpHirlTBYEka&DIc z3VrUClZ!@~SMt*=J2#Gs!sWf_V^8H#<`J# zJvh&}NRx!Sj^iL9qHMY~7On-t$3uD~JOWG^xHcFpbZzR^A1W9258c|+K3Um3*s_`A z4A-~&Tie=2Bu8={b1q|^h%Du(%UIySBF5vG5w&o)ZGr*XXKB2#P7}4nSQAgjEKIGysW|VXor5wK&dGF#o7IK8f+?YXHAF6XOcZ@6cIXa+8y~O%0i+ zJWt0A^#&n7AAAAr!$E(juBL~s>3}A}&|xT&kfuJ$hlBV$tHndINRRlgkO&`j0xGjr zyU+o42i0es=~zz3Zua;ov*VbMdmSpP{xRWB2L8`}dR^1Cd(SRuR}LGCY}%}_9rU*W zSD>Mm0XZSD7o{1Nm9fE+)Zk{!vj`$LLJvt6XJ{*#amLIsQ`|I{8TX1*Rui6JK-7SE zXmg>>rfi-{$xSDG*-&$)!ylO!e4~v;(*8}*=$k&VbeW-j;aW~T~+%d1NA zL>cBnMa#L0kusFC@xDbuF4`WBD5g5}UsW*Az3}rTLwl>Mfdn6_+2)`_Q*EygwZuvy zeQc^c%9(CpEK6Najiat*BJGN^OP;2I5>%d(YAn&o5_z=`6?Y|~`hwt;8w0Bf=cT&u zjkmyh&uhcm`hF2o=)=4SBP@GNpE@?gJ17MMd3#`uyt{x7K zS!~Z$9{#rdOv7kAZ8fw{H@uo{&g;SEU>z!X9cbj3rMj7!N>9v0LcU(Lop!6$b-Nwt zQa@OM!s&2kbhx8;Tpo6oZ9AZuI9w=Nrmo$r+<1NaHw{A@ww7vZB-ws6E3gOK8|&2^ zc?>@xW0~rPk+R54O-r)eP?pM*C}!MBRE}P?^2o?V#Pciy|Cm%8UUmM%=6b6#okN_NA!7y3%ghdc;V-aOZmYLjO8E&MC@=TYh z!pK#+V!O7@0D$BTZNJQQi*p}A4{B%zxhm-3442P)J)gN)zXBOB7#t4-Lp2H=gt&Mv z9iUMh3o+q~V$pEeord9i6Ip)OYbTAy_kCI_dzI}C*q)gU!{+*EG#Y4sMDVa*i)9kLFv`AjrE$RU!JYc$}0^G&lyiM z)8L7s6CPnH5t|}bg3c#h)@z^kSa+qp(r)@Lvjg^#Gd6<9Rs-$`_q4a_dT!J9oGwk3 z&Cwlre0Nn&Pe6njSOHGfR)EK0d*#nFE5Js7u)Z@Wb{^UR9;UM^Ja3hl677W*AXX7{ zNGvjr-5^Ub$xYLWEOym$dR{477#&oVwCSL%ST%rIx12(*Mf;KCqUvPPX+;Z);>{_} zWvdAzi*a7C9;Ufnmeke)!FF(Cb`O|z*5g$uPC%nhLP6m9|2eHuOy=NFj!1EYaJ>!uX$8DngIPkKRseUEr%W$m zWID-fm#xDl$9lNMu(j!c;7*|bV6yO5%(YbG(|2IY=b+QgsObG`Xq!AsQ0vJ!)h%7p z)Ni_7*K2XxYqkUmu_JgGuB_bScG@9v>eiw|nH$xiOjVEHsd+Ks)K1OYug}$E>Dh}7 zN=iom17Jj1j3Gv++l<-@Vo9_*zV9|$j?-#0n_8s5eY-Ba*&boI{R=doS~ATgy(Ti1xaagL8D6=?Q@4Azd$za&$UNul3S0F92it7G znB_1BLo^gk+ckVgFyDc-i#qAtV?(5P9h)*f+`KfZ&(X$Zde)*_MHXu6$;#zdYeKJC zv(3R63^q45Hnm4-v6%?GOzql^gIs%V?;hQ?>F|`FcKx6jor7b_y8i<$0*LkS8vp