# HG changeset patch
# User portiahollyoak
# Date 1463996441 14400
# Node ID eb2770895305e994a8fc3677cd3c48b84c2b8894
# Parent  8fee2dac93a436fb0b38e80dc32e37e0c49a6de2
planemo upload for repository https://github.com/portiahollyoak/Tools commit 6c005d5d29cd9684fee5474a7adac676fc27ecb3-dirty

diff -r 8fee2dac93a4 -r eb2770895305 test-data/X_1000000_Hum1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/X_1000000_Hum1.tab	Mon May 23 05:40:41 2016 -0400
@@ -0,0 +1,127 @@
+#Software: r2015.11-56-gbca69f3-unstable-dirty (commit r2015.11-56-gbca69f3-dirty)
+#Command: breakdancer-max breakdancer_config_X_100000 -g X_10000000_Hum1.bed 
+#Library Statistics:
+#X_10000000_Hum1.bam	mean:227	std:98	uppercutoff:521	lowercutoff:0	readlen:125	library:X_10000000_Hum1	reflen:999972	seqcov:11.8552	phycov:10.7645	1:62	2:3551	4:2764	8:106	32:1416
+#Chr1	Pos1	Orientation1	Chr2	Pos2	Orientation2	Type	Size	Score	num_Reads	num_Reads_lib	X_10000000_Hum1.bam
+X	131684	5+0-	X	131981	1+7-	DEL	340	65	5	X_10000000_Hum1.bam|5	2.98
+X	142444	7+4-	X	142488	7+4-	ITX	-102	67	4	X_10000000_Hum1.bam|4	NA
+X	142690	3+2-	X	142709	3+2-	ITX	-104	46	2	X_10000000_Hum1.bam|2	NA
+X	145921	3+0-	X	146395	0+2-	DEL	526	32	2	X_10000000_Hum1.bam|2	2.49
+X	151718	7+0-	X	151998	0+4-	DEL	331	41	4	X_10000000_Hum1.bam|4	3.95
+X	155647	5+3-	X	155671	5+3-	ITX	-102	60	3	X_10000000_Hum1.bam|3	NA
+X	157963	3+1-	X	158377	0+3-	DEL	432	35	3	X_10000000_Hum1.bam|3	4.62
+X	158261	4+4-	X	158489	0+6-	DEL	306	54	4	X_10000000_Hum1.bam|4	3.70
+X	159597	3+2-	X	159984	0+3-	DEL	437	35	3	X_10000000_Hum1.bam|3	2.29
+X	184550	2+4-	X	184570	2+4-	ITX	-107	45	2	X_10000000_Hum1.bam|2	NA
+X	185570	10+8-	X	185591	10+8-	ITX	-103	99	8	X_10000000_Hum1.bam|8	NA
+X	186648	9+18-	X	186959	6+6-	ITX	-171	74	6	X_10000000_Hum1.bam|6	0.95
+X	186648	9+18-	X	187326	18+8-	ITX	178	99	12	X_10000000_Hum1.bam|12	4.88
+X	186821	6+6-	X	187326	18+8-	ITX	20	38	4	X_10000000_Hum1.bam|4	4.55
+X	188119	11+2-	X	188178	11+2-	ITX	-104	32	2	X_10000000_Hum1.bam|2	NA
+X	188298	11+2-	X	188541	0+5-	DEL	326	34	3	X_10000000_Hum1.bam|3	2.15
+X	254834	1+10-	X	254884	1+10-	INV	-147	99	3	X_10000000_Hum1.bam|3	NA
+X	268244	7+1-	X	268508	7+7-	DEL	324	71	7	X_10000000_Hum1.bam|7	2.58
+X	268716	7+7-	X	269103	1+5-	DEL	446	47	5	X_10000000_Hum1.bam|5	5.24
+X	269032	2+2-	X	269471	0+2-	DEL	376	34	2	X_10000000_Hum1.bam|2	2.98
+X	269503	8+0-	X	269803	0+4-	DEL	306	45	3	X_10000000_Hum1.bam|3	2.51
+X	274164	4+4-	X	274175	4+4-	ITX	-105	95	4	X_10000000_Hum1.bam|4	NA
+X	280215	3+0-	X	280484	2+3-	DEL	321	33	3	X_10000000_Hum1.bam|3	2.39
+X	282107	13+0-	X	282350	0+13-	DEL	304	99	13	X_10000000_Hum1.bam|13	4.82
+X	295796	5+0-	X	303476	4+12-	DEL	7676	72	5	X_10000000_Hum1.bam|5	0.09
+X	295964	9+0-	X	303476	4+12-	DEL	7538	91	7	X_10000000_Hum1.bam|7	0.06
+X	307512	6+0-	X	307815	0+3-	DEL	321	43	3	X_10000000_Hum1.bam|3	2.54
+X	307512	6+0-	X	308007	0+10-	DEL	512	35	3	X_10000000_Hum1.bam|3	2.06
+X	316962	11+4-	X	317228	0+7-	DEL	383	61	7	X_10000000_Hum1.bam|7	4.48
+X	329258	9+4-	X	329314	9+4-	ITX	-102	61	4	X_10000000_Hum1.bam|4	NA
+X	332888	2+3-	X	332899	2+3-	ITX	-105	52	2	X_10000000_Hum1.bam|2	NA
+X	339370	4+0-	X	339690	0+4-	DEL	384	47	4	X_10000000_Hum1.bam|4	2.59
+X	343414	8+4-	X	343434	8+4-	ITX	-104	83	4	X_10000000_Hum1.bam|4	NA
+X	353226	4+6-	X	353254	4+6-	ITX	-102	76	4	X_10000000_Hum1.bam|4	NA
+X	358309	11+5-	X	358377	11+5-	ITX	-105	72	5	X_10000000_Hum1.bam|5	NA
+X	363873	2+0-	X	364155	0+2-	DEL	320	33	2	X_10000000_Hum1.bam|2	3.15
+X	366958	5+0-	X	367228	0+8-	DEL	319	48	5	X_10000000_Hum1.bam|5	2.33
+X	368221	4+2-	X	368271	4+2-	ITX	-102	34	2	X_10000000_Hum1.bam|2	NA
+X	393353	3+0-	X	393689	0+3-	DEL	405	37	3	X_10000000_Hum1.bam|3	2.91
+X	394653	8+5-	X	394702	8+5-	ITX	-104	81	5	X_10000000_Hum1.bam|5	NA
+X	394822	8+5-	X	395256	5+3-	DEL	452	34	3	X_10000000_Hum1.bam|3	2.97
+X	398500	3+4-	X	398517	3+4-	ITX	-104	66	3	X_10000000_Hum1.bam|3	NA
+X	399821	4+0-	X	400117	0+4-	DEL	347	57	4	X_10000000_Hum1.bam|4	1.93
+X	414461	5+1-	X	414833	3+2-	DEL	390	32	2	X_10000000_Hum1.bam|2	2.74
+X	418595	8+3-	X	418888	0+4-	DEL	355	40	4	X_10000000_Hum1.bam|4	5.21
+X	419577	3+3-	X	419588	3+3-	ITX	-105	52	2	X_10000000_Hum1.bam|2	NA
+X	426627	9+5-	X	426679	9+5-	ITX	-102	79	5	X_10000000_Hum1.bam|5	NA
+X	428545	14+0-	X	434702	0+8-	DEL	6151	59	5	X_10000000_Hum1.bam|5	0.06
+X	441688	7+12-	X	441764	7+12-	ITX	-105	85	6	X_10000000_Hum1.bam|6	NA
+X	445015	7+0-	X	445376	0+3-	DEL	390	57	3	X_10000000_Hum1.bam|3	4.91
+X	449622	3+0-	X	449909	0+3-	DEL	332	36	3	X_10000000_Hum1.bam|3	1.61
+X	456767	2+1-	X	457103	1+2-	DEL	354	41	2	X_10000000_Hum1.bam|2	3.61
+X	458386	6+2-	X	458412	6+2-	ITX	-103	42	2	X_10000000_Hum1.bam|2	NA
+X	471097	5+0-	X	471427	2+5-	DEL	348	43	3	X_10000000_Hum1.bam|3	3.28
+X	486082	4+3-	X	486116	4+3-	ITX	-103	55	3	X_10000000_Hum1.bam|3	NA
+X	488923	4+0-	X	489190	1+10-	DEL	335	39	4	X_10000000_Hum1.bam|4	4.03
+X	495979	7+1-	X	496291	0+3-	DEL	389	36	3	X_10000000_Hum1.bam|3	6.98
+X	496048	7+0-	X	496370	0+9-	DEL	434	44	4	X_10000000_Hum1.bam|4	6.25
+X	497786	7+5-	X	497877	7+5-	ITX	-103	51	4	X_10000000_Hum1.bam|4	NA
+X	503489	2+1-	X	503867	0+2-	DEL	404	42	2	X_10000000_Hum1.bam|2	3.35
+X	508754	2+9-	X	509277	8+0-	ITX	46	99	8	X_10000000_Hum1.bam|8	4.52
+X	508871	4+5-	X	508926	4+5-	ITX	-190	62	4	X_10000000_Hum1.bam|4	NA
+X	511090	6+0-	X	511323	9+5-	DEL	298	52	5	X_10000000_Hum1.bam|5	1.55
+X	525277	5+6-	X	525331	5+6-	ITX	-106	62	4	X_10000000_Hum1.bam|4	NA
+X	544176	3+2-	X	544203	3+2-	ITX	-103	41	2	X_10000000_Hum1.bam|2	NA
+X	547108	0+4-	X	547119	0+4-	INV	-172	99	2	X_10000000_Hum1.bam|2	NA
+X	576352	6+3-	X	576374	6+3-	ITX	-102	62	3	X_10000000_Hum1.bam|3	NA
+X	583435	4+2-	X	583796	0+4-	DEL	379	52	4	X_10000000_Hum1.bam|4	2.81
+X	606834	7+5-	X	606854	7+5-	ITX	-102	99	5	X_10000000_Hum1.bam|5	NA
+X	608448	3+1-	X	608799	2+3-	DEL	397	36	3	X_10000000_Hum1.bam|3	2.15
+X	608626	8+2-	X	608655	8+2-	ITX	-102	40	2	X_10000000_Hum1.bam|2	NA
+X	608775	8+2-	X	609044	5+3-	DEL	322	37	3	X_10000000_Hum1.bam|3	2.28
+X	608775	8+2-	X	609151	0+3-	DEL	348	39	3	X_10000000_Hum1.bam|3	2.51
+X	611710	7+8-	X	611742	7+8-	ITX	-103	99	6	X_10000000_Hum1.bam|6	NA
+X	616393	7+8-	X	616469	7+8-	ITX	-105	70	5	X_10000000_Hum1.bam|5	NA
+X	618395	6+0-	X	618664	0+4-	DEL	298	59	4	X_10000000_Hum1.bam|4	2.71
+X	636124	3+0-	X	636495	0+2-	DEL	320	39	2	X_10000000_Hum1.bam|2	2.71
+X	646679	0+5-	X	646771	0+5-	INV	-110	75	2	X_10000000_Hum1.bam|2	NA
+X	655838	5+4-	X	655862	5+4-	ITX	-105	79	4	X_10000000_Hum1.bam|4	NA
+X	661291	13+6-	X	661341	13+6-	ITX	-103	97	6	X_10000000_Hum1.bam|6	NA
+X	669443	7+6-	X	669472	7+6-	ITX	-105	99	6	X_10000000_Hum1.bam|6	NA
+X	679247	2+0-	X	679533	0+2-	DEL	320	36	2	X_10000000_Hum1.bam|2	1.77
+X	681969	6+0-	X	682249	0+6-	DEL	306	79	6	X_10000000_Hum1.bam|6	1.16
+X	686028	3+2-	X	686037	3+2-	ITX	-102	55	2	X_10000000_Hum1.bam|2	NA
+X	687744	7+4-	X	687842	7+4-	ITX	-105	37	3	X_10000000_Hum1.bam|3	NA
+X	693329	10+4-	X	693392	10+4-	ITX	-105	59	4	X_10000000_Hum1.bam|4	NA
+X	701901	5+12-	X	701966	5+12-	ITX	-103	74	5	X_10000000_Hum1.bam|5	NA
+X	701901	5+12-	X	703053	6+1-	ITX	617	78	6	X_10000000_Hum1.bam|6	4.21
+X	712176	6+9-	X	712264	6+9-	ITX	-102	66	5	X_10000000_Hum1.bam|5	NA
+X	729606	6+0-	X	729839	0+6-	DEL	296	73	6	X_10000000_Hum1.bam|6	1.55
+X	739865	3+1-	X	740260	0+2-	DEL	368	32	2	X_10000000_Hum1.bam|2	2.17
+X	745932	4+0-	X	746280	0+4-	DEL	384	65	4	X_10000000_Hum1.bam|4	3.24
+X	750098	7+3-	X	750122	7+3-	ITX	-102	60	3	X_10000000_Hum1.bam|3	NA
+X	769626	3+4-	X	769655	3+4-	ITX	-103	57	3	X_10000000_Hum1.bam|3	NA
+X	783709	4+2-	X	783748	4+2-	ITX	-103	37	2	X_10000000_Hum1.bam|2	NA
+X	801585	4+3-	X	801633	4+3-	ITX	-102	49	3	X_10000000_Hum1.bam|3	NA
+X	811468	13+13-	X	811480	13+13-	ITX	-105	99	13	X_10000000_Hum1.bam|13	NA
+X	812253	8+2-	X	817895	2+16-	DEL	5758	70	7	X_10000000_Hum1.bam|7	0.11
+X	812378	8+0-	X	817895	2+16-	DEL	5555	95	8	X_10000000_Hum1.bam|8	0.10
+X	819693	3+0-	X	820007	1+4-	DEL	369	33	3	X_10000000_Hum1.bam|3	2.28
+X	820478	8+5-	X	820521	8+5-	ITX	-105	84	5	X_10000000_Hum1.bam|5	NA
+X	821851	6+3-	X	821882	6+3-	ITX	-102	56	3	X_10000000_Hum1.bam|3	NA
+X	826401	2+3-	X	826801	1+2-	DEL	418	33	2	X_10000000_Hum1.bam|2	2.35
+X	827663	15+0-	X	835391	0+6-	DEL	7844	58	6	X_10000000_Hum1.bam|6	0.14
+X	827663	15+0-	X	835497	0+6-	DEL	7910	53	6	X_10000000_Hum1.bam|6	0.20
+X	836831	3+0-	X	837172	0+3-	DEL	375	44	3	X_10000000_Hum1.bam|3	2.33
+X	838911	2+3-	X	838923	2+3-	ITX	-104	51	2	X_10000000_Hum1.bam|2	NA
+X	842752	5+7-	X	842773	5+7-	ITX	-105	99	5	X_10000000_Hum1.bam|5	NA
+X	867585	3+2-	X	867902	0+3-	DEL	348	43	3	X_10000000_Hum1.bam|3	1.45
+X	869931	9+9-	X	869946	9+9-	ITX	-103	99	9	X_10000000_Hum1.bam|9	NA
+X	808851	0+5-	X	896693	0+5-	INV	87616	99	5	X_10000000_Hum1.bam|5	2.04
+X	882462	5+0-	X	882732	0+5-	DEL	311	55	5	X_10000000_Hum1.bam|5	3.24
+X	886628	7+0-	X	886945	2+7-	DEL	360	92	7	X_10000000_Hum1.bam|7	2.41
+X	893058	4+7-	X	893162	4+7-	ITX	-104	49	4	X_10000000_Hum1.bam|4	NA
+X	904956	6+0-	X	905302	0+5-	DEL	368	74	5	X_10000000_Hum1.bam|5	1.40
+X	906794	7+0-	X	908529	0+12-	DEL	1714	94	7	X_10000000_Hum1.bam|7	1.35
+X	922108	4+3-	X	922141	4+3-	ITX	-102	55	3	X_10000000_Hum1.bam|3	NA
+X	949787	3+2-	X	949812	3+2-	ITX	-103	42	2	X_10000000_Hum1.bam|2	NA
+X	970591	7+0-	X	970927	0+7-	DEL	319	87	7	X_10000000_Hum1.bam|7	2.77
+X	971930	3+5-	X	972019	3+5-	ITX	-102	39	3	X_10000000_Hum1.bam|3	NA
+X	976376	7+0-	X	976723	0+7-	DEL	419	78	7	X_10000000_Hum1.bam|7	1.99
+X	999900	11+3-	X	999950	11+3-	ITX	-104	48	3	X_10000000_Hum1.bam|3	NA
diff -r 8fee2dac93a4 -r eb2770895305 test-data/breakdancer_config_X_100000
--- a/test-data/breakdancer_config_X_100000	Mon May 23 05:19:22 2016 -0400
+++ b/test-data/breakdancer_config_X_100000	Mon May 23 05:40:41 2016 -0400
@@ -1,1 +1,1 @@
-map:../HUM_BAM_dm6fasta/Hum1.bwa.bam	mean:227	std:98	readlen:125	sample:HUM1	exe:samtools view
+map:X_10000000_Hum1.bam	mean:227	std:98	readlen:125	sample:X_10000000_Hum1	exe:samtools view