Mercurial > repos > devteam > pileup_parser

diff test-data/pileup_parser.6col.pileup @ 0:ff1ba9b75337 draft

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Uploaded tool tarball.
author devteam
date Mon, 26 Aug 2013 15:14:34 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pileup_parser.6col.pileup	Mon Aug 26 15:14:34 2013 -0400
@@ -0,0 +1,1000 @@
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+chrM	581	G	3	..,	III
+chrM	582	C	3	..,	II?
+chrM	583	C	3	..a	II-
+chrM	584	T	3	..,	IIH
+chrM	585	A	3	..,	III
+chrM	586	A	3	..,	III
+chrM	587	A	4	..,^:,	IIII
+chrM	588	A	4	..,,	IIII
+chrM	589	C	4	..,,	IIII
+chrM	590	T	4	..,,	II.5
+chrM	591	C	4	.$.,,	II<I
+chrM	592	A	3	.,,	III
+chrM	593	A	3	.,,	III
+chrM	594	A	3	.,,	III
+chrM	595	G	3	.,,	III
+chrM	596	G	3	.,,	III
+chrM	597	A	3	.,,	:EI
+chrM	598	C	3	.,,	III
+chrM	599	T	4	.,,^:.	II@I
+chrM	600	T	4	.,,.	IIII
+chrM	601	G	4	.,,.	IIII
+chrM	602	G	4	.,,.	IIII
+chrM	603	C	4	.,,.	IIII
+chrM	604	G	4	.,,.	IIII
+chrM	605	G	4	.,,.	IIII
+chrM	606	T	4	.,,.	5III
+chrM	607	G	4	.,,.	IIII
+chrM	608	C	4	.,,.	*III
+chrM	609	T	5	.,,.^:,	?IIII
+chrM	610	T	5	.,,.,	IIII8
+chrM	611	T	5	.,,.,	IIIII
+chrM	612	A	5	T$,,.,	3IIII
+chrM	613	C	4	,,.,	III)
+chrM	614	A	4	,,.,	IIII
+chrM	615	T	4	,$,.,	IIII
+chrM	616	C	3	,.,	III
+chrM	617	C	3	,.,	III
+chrM	618	C	3	,.,	III
+chrM	619	T	3	,.,	IF9
+chrM	620	C	3	,.,	II7
+chrM	621	T	3	,.,	III
+chrM	622	A	3	,$.,	I7I
+chrM	623	G	2	.,	II
+chrM	624	A	2	.,	9I
+chrM	625	G	2	.,	II
+chrM	626	G	2	.,	II
+chrM	627	A	2	.,	2I
+chrM	628	G	2	.,	II
+chrM	629	C	2	.,	II
+chrM	630	C	2	.,	II
+chrM	631	T	2	.,	II
+chrM	632	G	2	.,	II
+chrM	633	T	2	.,	II
+chrM	634	T	2	.$,	II
+chrM	635	C	1	,	I
+chrM	636	C	1	,	I
+chrM	637	A	1	,	I
+chrM	638	T	1	,	I
+chrM	639	A	1	,	I
+chrM	640	A	1	,	I
+chrM	641	T	1	,	I
+chrM	642	C	1	,	I
+chrM	643	G	1	,	I
+chrM	644	A	1	,$	I
+chrM	646	A	1	^:.	I
+chrM	647	A	1	.	I
+chrM	648	A	1	.	I
+chrM	649	C	2	.^:,	II
+chrM	650	C	2	.,	II
+chrM	651	C	2	.,	II
+chrM	652	C	3	.,^:,	II)
+chrM	653	G	3	.,,	II2
+chrM	654	A	3	.,,	III
+chrM	655	T	4	.,,^:.	II*I
+chrM	656	A	4	.,,.	IIII
+chrM	657	A	4	.,,.	IIII
+chrM	658	A	4	.,,.	IIII
+chrM	659	C	4	.,,.	IIII
+chrM	660	C	4	.,,.	IIII
+chrM	661	C	4	.,,.	IIII
+chrM	662	C	4	.,,.	IIFI
+chrM	663	A	4	.,,.	=IDI
+chrM	664	C	4	.,,.	II6I
+chrM	665	C	5	.,,.^:,	IIIII
+chrM	666	A	5	.,,.,	BIIII
+chrM	667	T	5	.,,.,	II5I+
+chrM	668	C	5	.,,.,	IIIII
+chrM	669	C	5	.,,.,	IIIII
+chrM	670	C	5	.,a.,	II.II
+chrM	671	T	5	.,,.,	IIIIA
+chrM	672	T	6	.,,.,^:.	FI9I.I
+chrM	673	G	6	.,,.,.	IIIIII
+chrM	674	C	6	.,,.,.	IIIIII
+chrM	675	T	6	.,,.,.	IIIIII
+chrM	676	A	6	.,,.,.	,IIEII
+chrM	677	A	7	.,,.,.^:.	3II;III
+chrM	678	T	7	.,,.,..	IIIIDII
+chrM	679	T	7	.,,.,..	CIIIIII
+chrM	680	C	7	.,,.,..	IIIIIII
+chrM	681	A	7	.$,,.,..	9IIIIII
+chrM	682	G	6	,,.,..	II$III
+chrM	683	C	6	,,.,..	IIIIII
+chrM	684	C	6	,$,.,..	IIIIII
+chrM	685	T	5	,.,..	IIIII
+chrM	686	A	5	,.,..	IIIII
+chrM	687	T	5	,$.,..	IIIII
+chrM	688	A	4	.,..	IIII
+chrM	689	T	4	.,..	IIII
+chrM	690	A	4	.$,..	IIII
+chrM	691	C	3	,..	III
+chrM	692	C	3	,..	III
+chrM	693	G	4	,..^:,	IIII
+chrM	694	C	4	,..,	IIII
+chrM	695	C	4	,..,	IIII
+chrM	696	A	4	,..,	IIII
+chrM	697	T	4	,..,	IIII
+chrM	698	C	4	,..,	IIII
+chrM	699	T	4	,..,	IIII
+chrM	700	T	4	,$..,	IIII
+chrM	701	C	3	..,	III
+chrM	702	A	3	..,	III
+chrM	703	G	3	..,	2II
+chrM	704	C	3	..,	III
+chrM	705	A	3	N.,	"II
+chrM	706	A	3	..,	I5I
+chrM	707	A	3	.$.,	GII
+chrM	708	C	2	.,	II
+chrM	709	C	2	.,	II
+chrM	710	C	2	.,	II
+chrM	711	T	2	.,	II
+chrM	712	A	2	.$,	II
+chrM	713	A	1	,	I
+chrM	714	A	1	,	I
+chrM	715	C	1	,	I
+chrM	716	A	1	,	I
+chrM	717	A	1	,	I
+chrM	718	G	1	,	I
+chrM	719	G	2	,^:,	I&
+chrM	720	T	2	,g	I$
+chrM	721	A	2	,,	I3
+chrM	722	C	2	,,	I$
+chrM	723	C	2	,t	I&
+chrM	724	G	2	,,	I)
+chrM	725	A	2	,,	II
+chrM	726	A	3	,,^:.	III
+chrM	727	G	3	,,.	III
+chrM	728	T	3	,$,.	III
+chrM	729	A	2	,.	II
+chrM	730	A	2	n.	"I
+chrM	731	G	2	,.	II
+chrM	732	C	3	a.^:.	$II
+chrM	733	A	3	,..	III
+chrM	734	C	3	,..	%II
+chrM	735	A	3	,..	III
+chrM	736	A	3	,..	*II
+chrM	737	A	3	,..	III
+chrM	738	T	3	,..	III
+chrM	739	A	3	,..	III
+chrM	740	T	3	,..	III
+chrM	741	C	3	,..	III
+chrM	742	C	3	,..	III
+chrM	743	A	3	,..	III
+chrM	744	A	3	,..	III
+chrM	745	C	3	,..	III
+chrM	746	A	3	,..	IIE
+chrM	747	T	3	,..	III
+chrM	748	A	3	,..	III
+chrM	749	A	3	,..	III
+chrM	750	A	3	,..	III
+chrM	751	A	3	,..	IAI
+chrM	752	A	3	,..	III
+chrM	753	C	3	,..	III
+chrM	754	G	3	,$..	III
+chrM	755	T	2	..	II
+chrM	756	T	3	..^:,	III
+chrM	757	A	3	..,	III
+chrM	758	G	3	..,	III
+chrM	759	G	3	..,	III
+chrM	760	T	3	..,	=II
+chrM	761	C	3	.$.,	IID
+chrM	762	A	2	.,	=I
+chrM	763	A	2	.,	EI
+chrM	764	G	2	.,	II
+chrM	765	G	2	.,	II
+chrM	766	T	2	.,	:I
+chrM	767	G	3	.$,^:,	III
+chrM	768	T	2	,,	I>
+chrM	769	A	3	,,^:,	III
+chrM	770	G	3	,,,	III
+chrM	771	C	3	,,,	IHI
+chrM	772	C	3	,a,	I)/
+chrM	773	C	3	,,,	I7I
+chrM	774	A	4	,,,^:.	II:I
+chrM	775	T	4	,,,.	IH.I
+chrM	776	G	4	,,,.	IIII
+chrM	777	G	4	,,,.	IIII
+chrM	778	G	4	,,,.	IIII
+chrM	779	A	4	,,,.	IIAI
+chrM	780	T	4	,,,.	IIGI
+chrM	781	G	4	,,,.	IIII
+chrM	782	G	4	,,,.	IIII
+chrM	783	A	4	,,,.	IIII
+chrM	784	G	4	,,,.	IIII
+chrM	785	A	4	,,,.	IIII
+chrM	786	G	4	,,,.	IIII
+chrM	787	A	4	,,,.	IIII
+chrM	788	A	4	,,,.	IIII
+chrM	789	A	4	,,,.	IIII
+chrM	790	T	5	,,,.^:.	IIIII
+chrM	791	G	5	,$,,..	IIIII
+chrM	792	G	4	,,..	IIII
+chrM	793	G	4	,,..	IIII
+chrM	794	C	4	,,..	IIII
+chrM	795	T	4	,,..	IIII
+chrM	796	A	4	,,..	IIII
+chrM	797	C	4	,,..	IIII
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+chrM	799	T	4	,,..	IIII
+chrM	800	T	4	,,..	IIII
+chrM	801	T	4	,,..	IIII
+chrM	802	T	4	,$,..	IIII
+chrM	803	C	3	,..	III
+chrM	804	T	3	,$..	III
+chrM	805	A	2	..	II
+chrM	806	C	3	..^:.	III
+chrM	807	C	3	...	III
+chrM	808	C	3	...	III
+chrM	809	T	3	.$..	III
+chrM	810	A	3	..^:,	III
+chrM	811	A	3	..,	III
+chrM	812	G	3	..,	II7
+chrM	813	A	3	..,	III
+chrM	814	A	3	..,	III
+chrM	815	C	3	..,	III
+chrM	816	A	3	..,	III
+chrM	817	A	3	..,	III
+chrM	818	G	3	..,	III
+chrM	819	A	3	..,	III
+chrM	820	A	3	..,	&II
+chrM	821	C	3	..,	III
+chrM	822	T	3	..,	III
+chrM	823	T	3	..n	II"
+chrM	824	T	3	..,	III
+chrM	825	A	3	.$.,	III
+chrM	826	A	3	.,^:.	III
+chrM	827	C	3	.,.	III
+chrM	828	C	3	.,.	III
+chrM	829	C	4	.,.^:,	IIII
+chrM	830	G	4	.,.,	IIII
+chrM	831	G	4	.,.,	IIII
+chrM	832	A	4	.,.,	IIII
+chrM	833	C	4	.,.,	IIII
+chrM	834	G	4	.,.,	IIII
+chrM	835	A	4	.,.,	IIII
+chrM	836	A	4	.,.,	8III
+chrM	837	A	4	.,.,	IIII
+chrM	838	G	4	.,.,	IIII
+chrM	839	T	5	.,.,^:,	4:IIG
+chrM	840	C	5	.,.,,	IIIII
+chrM	841	T	5	.$,.,,	IIIII
+chrM	842	C	4	,.,,	IIII
+chrM	843	C	4	,.,,	IIII
+chrM	844	A	4	,.,,	IIII
+chrM	845	T	4	,$.,,	IIII
+chrM	846	G	3	.,,	@II
+chrM	847	A	3	.,,	III
+chrM	848	A	3	.,,	III
+chrM	849	A	3	.,,	III
+chrM	850	C	3	.,,	III
+chrM	851	T	3	.,,	III
+chrM	852	G	3	.,,	III
+chrM	853	G	3	.,,	III
+chrM	854	A	3	.,,	EII
+chrM	855	G	3	.,,	DII
+chrM	856	A	3	.,,	III
+chrM	857	C	3	.,,	III
+chrM	858	T	4	.,,^:,	IIIA
+chrM	859	A	4	.,,,	@III
+chrM	860	A	4	.,,,	IIII
+chrM	861	A	4	.$,,,	EIII
+chrM	862	G	3	,,,	III
+chrM	863	G	3	,,,	III
+chrM	864	A	3	,$,,	III
+chrM	865	G	2	,,	II
+chrM	866	G	2	,,	II
+chrM	867	A	2	,,	II
+chrM	868	T	2	,,	II
+chrM	869	T	2	,,	II
+chrM	870	T	2	,,	II
+chrM	871	A	2	,,	II
+chrM	872	G	2	,,	II
+chrM	873	C	2	,,	II
+chrM	874	A	2	,$,	II
+chrM	875	G	1	,	I
+chrM	876	T	1	,	I
+chrM	877	A	1	,	I
+chrM	878	A	1	,	I
+chrM	879	A	1	,	I
+chrM	880	T	1	,	I
+chrM	881	T	1	,	I
+chrM	882	A	1	,	I
+chrM	883	A	1	,	I
+chrM	884	G	1	,	I
+chrM	885	A	1	,	I
+chrM	886	A	1	,	I
+chrM	887	T	1	,	(
+chrM	888	A	1	,	I
+chrM	889	G	1	,	I
+chrM	890	A	1	,	I
+chrM	891	G	1	,	I
+chrM	892	A	1	,	I
+chrM	893	G	1	,$	I
+chrM	898	A	1	^:,	I
+chrM	899	T	2	,^:.	/I
+chrM	900	T	2	,.	7I
+chrM	901	G	2	,.	CI
+chrM	902	A	2	,.	II
+chrM	903	A	2	,.	II
+chrM	904	T	2	,.	II
+chrM	905	C	3	,.^:,	III
+chrM	906	A	3	,.,	III
+chrM	907	G	3	,.,	III
+chrM	908	G	3	,.,	III
+chrM	909	C	3	,.,	III
+chrM	910	C	3	,.,	III
+chrM	911	A	4	,.,^:,	IIII
+chrM	912	T	4	,.,,	IIEG
+chrM	913	G	4	,.,,	III:
+chrM	914	A	4	,.,,	IIII
+chrM	915	A	4	,.,,	IIII
+chrM	916	G	4	,.,,	III5
+chrM	917	C	4	,.,,	III5
+chrM	918	G	4	,.,,	IIII
+chrM	919	C	4	,.,,	III<
+chrM	920	G	4	,.,,	IIII
+chrM	921	C	4	,.,,	IIII
+chrM	922	A	4	,.,,	IIII
+chrM	923	C	4	,.,,	III8
+chrM	924	A	4	,.,,	IFII
+chrM	925	C	4	,.,,	IIII
+chrM	926	A	4	,.,,	IIII
+chrM	927	C	4	,.,,	IIII
+chrM	928	C	5	,.,,^:,	IIII:
+chrM	929	G	5	,.,,,	IIIE:
+chrM	930	C	5	,.,,,	IIIII
+chrM	931	C	5	,.,,,	IIIIF
+chrM	932	C	5	,.,,,	IIIIC
+chrM	933	G	5	,$.,,,	I?II:
+chrM	934	T	4	.$,,,	4II>
+chrM	935	C	3	,,,	III
+chrM	936	A	3	,,,	III
+chrM	937	C	3	,,,	II1
+chrM	938	C	3	,,,	III
+chrM	939	C	3	,,,	III
+chrM	940	T	3	,$,,	III
+chrM	941	C	2	,,	II
+chrM	942	C	2	,,	I'
+chrM	943	T	2	,,	II
+chrM	944	T	2	,,	II
+chrM	945	A	2	,,	II
+chrM	946	A	2	,$,	II
+chrM	947	A	1	,	I
+chrM	948	T	1	,	I
+chrM	949	A	1	,	I
+chrM	950	T	1	,	I
+chrM	951	C	1	,	I
+chrM	952	A	1	,	I
+chrM	953	C	1	,	I
+chrM	954	A	1	,	I
+chrM	955	A	2	,^:.	II
+chrM	956	A	2	,.	II
+chrM	957	T	2	,.	II
+chrM	958	C	3	,.^:.	III
+chrM	959	A	3	,..	III
+chrM	960	T	3	,..	III
+chrM	961	A	3	,..	III
+chrM	962	A	3	,..	III
+chrM	963	C	4	,$..^:.	IIII
+chrM	964	A	3	...	I(;
+chrM	965	T	3	...	III
+chrM	966	A	4	...^:.	IIII
+chrM	967	A	4	....	IIII
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+chrM	969	A	4	....	IIII
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+chrM	971	A	4	....	IIII
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+chrM	974	A	5	....^:.	IIIII
+chrM	975	C	5	.....	IIIII
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+chrM	977	G	5	.....	IIIII
+chrM	978	T	5	.....	IIIII
+chrM	979	G	5	.....	I0III
+chrM	980	A	5	.....	IIII4
+chrM	981	C	5	.....	IIIII
+chrM	982	C	5	.....	IIIII
+chrM	983	C	5	.....	IIIII
+chrM	984	A	5	.....	-IGII
+chrM	985	A	5	.....	4GIII
+chrM	986	A	5	.....	BDGII
+chrM	987	C	5	.....	IDIII
+chrM	988	A	5	.....	@<III
+chrM	989	T	5	.....	IIIII
+chrM	990	A	5	.$....	I@III
+chrM	991	T	4	....	IICI
+chrM	992	G	4	T...	)III
+chrM	993	A	4	.$...	?ICI
+chrM	994	A	3	...	III
+chrM	995	A	3	...	III
+chrM	996	G	3	...	III
+chrM	997	G	3	...	III
+chrM	998	A	3	.$..	4II
+chrM	999	G	3	..^:.	III
+chrM	1000	A	3	...	III
+chrM	1001	C	3	.$..	III
+chrM	1002	A	2	..	II
+chrM	1003	A	2	..	II
+chrM	1004	G	2	..	II
+chrM	1005	T	2	..	II
+chrM	1006	C	2	..	II
+chrM	1007	G	2	..	CI
+chrM	1008	T	2	..	II
+chrM	1009	A	2	.$.	II
+chrM	1010	A	1	.	I
+chrM	1011	C	1	.	I
+chrM	1012	A	1	.	I
+chrM	1013	A	1	.	I
+chrM	1014	G	1	.	I
+chrM	1015	G	1	.	I
+chrM	1016	T	1	.	I
+chrM	1017	A	1	.	I
+chrM	1018	A	1	.	I
+chrM	1019	G	1	.	I
+chrM	1020	T	1	.	I
+chrM	1021	A	1	.	I
+chrM	1022	T	1	.	I
+chrM	1023	A	1	.	I
+chrM	1024	C	1	.	I
+chrM	1025	C	1	.	I
+chrM	1026	G	1	.	I
+chrM	1027	G	1	.	I
+chrM	1028	A	1	.	I
+chrM	1029	A	1	.	I
+chrM	1030	G	1	.	I
+chrM	1031	G	2	.^:.	II
+chrM	1032	T	2	..	EI
+chrM	1033	G	2	..	II
+chrM	1034	T	2	.$.	II
+chrM	1035	A	2	.^:.	II
+chrM	1036	C	2	..	II
+chrM	1037	T	2	..	II
+chrM	1038	T	2	..	II
+chrM	1039	G	2	..	II
+chrM	1040	G	2	..	II
+chrM	1041	A	2	..	II
+chrM	1042	T	2	..	II
+chrM	1043	A	3	..^:,	III
+chrM	1044	A	3	..,	III
+chrM	1045	C	3	..,	II7
+chrM	1046	C	3	..,	II-
+chrM	1047	A	3	..,	III
+chrM	1048	A	3	..,	III
+chrM	1049	A	3	..,	III
+chrM	1050	G	3	..,	III
+chrM	1051	T	3	..,	III
+chrM	1052	G	3	..,	III
+chrM	1053	T	3	..,	GII
+chrM	1054	A	3	..,	III
+chrM	1055	G	3	..,	:II
+chrM	1056	C	3	..a	HI%
+chrM	1057	T	3	..,	III
+chrM	1058	T	3	..,	III
+chrM	1059	A	3	..,	BII
+chrM	1060	A	3	..,	GII
+chrM	1061	A	3	..,	HII
+chrM	1062	C	3	..,	III
+chrM	1063	A	3	..,	DII
+chrM	1064	A	3	..,	BII
+chrM	1065	A	3	..,	1II
+chrM	1066	G	3	.$.,	&II
+chrM	1067	C	2	.,	II
+chrM	1068	A	2	.,	II
+chrM	1069	T	2	.,	II
+chrM	1070	C	2	.$,	II
+chrM	1071	C	1	,	I
+chrM	1072	A	1	,	I
+chrM	1073	G	1	,	I
+chrM	1074	C	1	,	I
+chrM	1075	T	1	,	I
+chrM	1076	T	1	,	I
+chrM	1077	A	1	,	I
+chrM	1078	C	1	,$	I
+chrM	1090	T	1	^:,	I
+chrM	1091	T	1	,	I
+chrM	1092	C	1	n	"
+chrM	1093	A	1	,	I
+chrM	1094	C	1	,	I
+chrM	1095	T	1	,	7
+chrM	1096	C	1	a	B
+chrM	1097	A	1	,	I
+chrM	1098	A	1	,	I
+chrM	1099	A	1	,	I
+chrM	1100	A	1	,	I
+chrM	1101	T	1	,	I
+chrM	1102	G	2	,^:,	(I
+chrM	1103	A	2	,,	II
+chrM	1104	A	2	,,	I+
+chrM	1105	C	2	,,	.I
+chrM	1106	A	2	,,	8I