--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnaseq/cutadapt/test-data/blat_wrapper_test1.out	Sat Feb 21 16:33:42 2015 +0100
@@ -0,0 +1,64 @@
+30	0	0	0	0	0	0	0	+	0_0.666667	30	0	30	chr	4639675	4549207	4549237	1	30,	0,	4549207,	cggacagcgccgccaccaacaaagccacca,	cggacagcgccgccaccaacaaagccacca,
+30	0	0	0	0	0	0	0	+	1_0.600000	30	0	30	chr	4639675	614777	614807	1	30,	0,	614777,	aaaacaccggatgctccggcgctggcagat,	aaaacaccggatgctccggcgctggcagat,
+28	1	0	0	0	0	0	0	+	2_0.400000	30	0	29	chr	4639675	3289283	3289312	1	29,	0,	3289283,	tttgcttttagtacaccggattcagaacc,	tttgctttcagtacaccggattcagaacc,
+30	0	0	0	0	0	0	0	+	4_0.766667	30	0	30	chr	4639675	2665584	2665614	1	30,	0,	2665584,	cacgctacgtgcgcccccgcccagaaggcg,	cacgctacgtgcgcccccgcccagaaggcg,
+20	0	0	0	0	0	0	0	+	5_0.533333	30	4	24	chr	4639675	3375780	3375800	1	20,	4,	3375780,	aaaacccgccgaagcgggtt,	aaaacccgccgaagcgggtt,
+30	0	0	0	0	0	0	0	+	6_0.533333	30	0	30	chr	4639675	965481	965511	1	30,	0,	965481,	taagccgttactggcagcaagtgcaggcaa,	taagccgttactggcagcaagtgcaggcaa,
+30	0	0	0	0	0	0	0	+	7_0.400000	30	0	30	chr	4639675	1781311	1781341	1	30,	0,	1781311,	tgaatttaccgttatctatcttgcctgcct,	tgaatttaccgttatctatcttgcctgcct,
+29	1	0	0	0	0	0	0	+	9_0.400000	30	0	30	chr	4639675	4400977	4401007	1	30,	0,	4400977,	gcgttttgctaaacttctgccggaatataa,	gcgctttgctaaacttctgccggaatataa,
+30	0	0	0	0	0	0	0	+	11_0.533333	30	0	30	chr	4639675	3923551	3923581	1	30,	0,	3923551,	caaaagcagagtctgttgacccatacgcgc,	caaaagcagagtctgttgacccatacgcgc,
+28	2	0	0	0	0	0	0	+	12_0.700000	30	0	30	chr	4639675	3304453	3304483	1	30,	0,	3304453,	gcggacgatcttcacggtcgccacgcggac,	gcggacgatcttcacggtcaccacgcgggc,
+29	1	0	0	0	0	0	0	+	13_0.533333	30	0	30	chr	4639675	4555547	4555577	1	30,	0,	4555547,	ttcttgttggatggcatactccggcagcca,	ttcttgttggatggcgtactccggcagcca,
+30	0	0	0	0	0	0	0	+	14_0.666667	30	0	30	chr	4639675	3811672	3811702	1	30,	0,	3811672,	accccgatatcgtcgcaggcgttgccgcac,	accccgatatcgtcgcaggcgttgccgcac,
+29	1	0	0	0	0	0	0	+	16_0.566667	30	0	30	chr	4639675	1916143	1916173	1	30,	0,	1916143,	atgtcctgatcgagcggcgttttaccgacc,	atgtcctgatcgagcggcgttttaccgatc,
+30	0	0	0	0	0	0	0	+	18_0.566667	30	0	30	chr	4639675	1860631	1860661	1	30,	0,	1860631,	gtggtctcaagcccaaaggaagagtgaggc,	gtggtctcaagcccaaaggaagagtgaggc,
+30	0	0	0	0	0	0	0	+	19_0.566667	30	0	30	chr	4639675	1018466	1018496	1	30,	0,	1018466,	gttgtaagcgtcagaaccgatgcggtcggt,	gttgtaagcgtcagaaccgatgcggtcggt,
+30	0	0	0	0	0	0	0	+	22_0.566667	30	0	30	chr	4639675	2006716	2006746	1	30,	0,	2006716,	cggtattcctcagttctcgctgcatgcctg,	cggtattcctcagttctcgctgcatgcctg,
+30	0	0	0	0	0	0	0	-	23_0.600000	30	0	30	chr	4639675	4516584	4516614	1	30,	0,	4516584,	cgctactgaaggcgtggtgcgtaacggcaa,	cgctactgaaggcgtggtgcgtaacggcaa,
+30	0	0	0	0	0	0	0	-	24_0.733333	30	0	30	chr	4639675	1535123	1535153	1	30,	0,	1535123,	gaacagcagcagcgacgtggtgcgcccgcg,	gaacagcagcagcgacgtggtgcgcccgcg,
+30	0	0	0	0	0	0	0	+	27_0.600000	30	0	30	chr	4639675	3442475	3442505	1	30,	0,	3442475,	ttaccgaggccagaaccgataccacgaccc,	ttaccgaggccagaaccgataccacgaccc,
+29	1	0	0	0	0	0	0	+	29_0.700000	30	0	30	chr	4639675	2807120	2807150	1	30,	0,	2807120,	ctcgtccggcgggcggttttgccgacaagg,	ctcgtccggcgggcggttttgccgataagg,
+30	0	0	0	0	0	0	0	+	34_0.533333	30	0	30	chr	4639675	421739	421769	1	30,	0,	421739,	tgatgttaaatgcatggcacctgccggtgc,	tgatgttaaatgcatggcacctgccggtgc,
+30	0	0	0	0	0	0	0	-	35_0.466667	30	0	30	chr	4639675	1334399	1334429	1	30,	0,	1334399,	ggttaacctcgaatatctcggcaaagcagt,	ggttaacctcgaatatctcggcaaagcagt,
+30	0	0	0	0	0	0	0	+	36_0.433333	30	0	30	chr	4639675	2906502	2906532	1	30,	0,	2906502,	tgttggcaacatggcgagcgtaatcaatta,	tgttggcaacatggcgagcgtaatcaatta,
+30	0	0	0	0	0	0	0	+	38_0.533333	30	0	30	chr	4639675	3438288	3438318	1	30,	0,	3438288,	gcagcaggatcggatcgaactctggtttct,	gcagcaggatcggatcgaactctggtttct,
+29	1	0	0	0	0	0	0	+	39_0.400000	30	0	30	chr	4639675	2893756	2893786	1	30,	0,	2893756,	taatgcggcattctcctgatttattgtcac,	tattgcggcattctcctgatttattgtcac,
+29	0	0	0	0	0	0	0	+	41_0.566667	30	1	30	chr	4639675	708504	708533	1	29,	1,	708504,	gctgacggtcagcagggatacttcctgca,	gctgacggtcagcagggatacttcctgca,
+30	0	0	0	0	0	0	0	+	43_0.466667	30	0	30	chr	4639675	3483475	3483505	1	30,	0,	3483475,	gctttttccagcatcaacgccactgaacaa,	gctttttccagcatcaacgccactgaacaa,
+30	0	0	0	0	0	0	0	+	44_0.433333	30	0	30	chr	4639675	4590702	4590732	1	30,	0,	4590702,	aaagtggtagataacgtggtgcagactatg,	aaagtggtagataacgtggtgcagactatg,
+30	0	0	0	0	0	0	0	+	49_0.433333	30	0	30	chr	4639675	3341305	3341335	1	30,	0,	3341305,	cgttatacggaacaacatttaactccagcg,	cgttatacggaacaacatttaactccagcg,
+28	2	0	0	0	0	0	0	+	50_0.466667	30	0	30	chr	4639675	2777224	2777254	1	30,	0,	2777224,	ttgctgttgccatcgcttttcaggacatac,	ttgctgttgccgtcacttttcaggacatac,
+30	0	0	0	0	0	0	0	+	53_0.533333	30	0	30	chr	4639675	1768655	1768685	1	30,	0,	1768655,	ccaggcactccgccatatttttgccatgac,	ccaggcactccgccatatttttgccatgac,
+30	0	0	0	0	0	0	0	+	54_0.400000	30	0	30	chr	4639675	2359543	2359573	1	30,	0,	2359543,	gtattcttcattgatttgtaagcgggtacc,	gtattcttcattgatttgtaagcgggtacc,
+30	0	0	0	0	0	0	0	+	57_0.566667	30	0	30	chr	4639675	256715	256745	1	30,	0,	256715,	cgcgaaatcctcgacgtccaggcacgtatt,	cgcgaaatcctcgacgtccaggcacgtatt,
+30	0	0	0	0	0	0	0	+	58_0.300000	30	0	30	chr	4639675	1108478	1108508	1	30,	0,	1108478,	gttatccattaaaatagatcggatcgatat,	gttatccattaaaatagatcggatcgatat,
+30	0	0	0	0	0	0	0	+	60_0.533333	30	0	30	chr	4639675	1130738	1130768	1	30,	0,	1130738,	aatctggcgaatgctgatagcgtgaccggt,	aatctggcgaatgctgatagcgtgaccggt,
+30	0	0	0	0	0	0	0	-	61_0.366667	30	0	30	chr	4639675	1578065	1578095	1	30,	0,	1578065,	aaaaaacggctgacaaagctttcaaactga,	aaaaaacggctgacaaagctttcaaactga,
+30	0	0	0	0	0	0	0	+	63_0.566667	30	0	30	chr	4639675	3422447	3422477	1	30,	0,	3422447,	tcacgctcgcagtcaagctggcttatgcca,	tcacgctcgcagtcaagctggcttatgcca,
+30	0	0	0	0	0	0	0	+	63_0.566667	30	0	30	chr	4639675	2724848	2724878	1	30,	0,	2724848,	tcacgctcgcagtcaagctggcttatgcca,	tcacgctcgcagtcaagctggcttatgcca,
+30	0	0	0	0	0	0	0	-	63_0.566667	30	0	30	chr	4639675	4210393	4210423	1	30,	0,	4210393,	tggcataagccagcttgactgcgagcgtga,	tggcataagccagcttgactgcgagcgtga,
+30	0	0	0	0	0	0	0	-	63_0.566667	30	0	30	chr	4639675	3944054	3944084	1	30,	0,	3944054,	tggcataagccagcttgactgcgagcgtga,	tggcataagccagcttgactgcgagcgtga,
+29	1	0	0	0	0	0	0	+	64_0.500000	30	0	30	chr	4639675	4553565	4553595	1	30,	0,	4553565,	gagatgacggttgcagagtcatgcgtttga,	gagatgacggttgcagagtcatacgtttga,
+30	0	0	0	0	0	0	0	+	65_0.533333	30	0	30	chr	4639675	3154209	3154239	1	30,	0,	3154209,	tctggatcacgcgcaaacactggctatcgt,	tctggatcacgcgcaaacactggctatcgt,
+30	0	0	0	0	0	0	0	+	66_0.466667	30	0	30	chr	4639675	3330950	3330980	1	30,	0,	3330950,	tctgctttagcaaacagagtgtggtcacga,	tctgctttagcaaacagagtgtggtcacga,
+30	0	0	0	0	0	0	0	+	68_0.566667	30	0	30	chr	4639675	699412	699442	1	30,	0,	699412,	gaaggatagttggtcagcaacaccagcggc,	gaaggatagttggtcagcaacaccagcggc,
+30	0	0	0	0	0	0	0	+	69_0.733333	30	0	30	chr	4639675	3218070	3218100	1	30,	0,	3218070,	ggcgcgctgtcggccacggcgaaatcgacc,	ggcgcgctgtcggccacggcgaaatcgacc,
+29	1	0	0	0	0	0	0	+	72_0.533333	30	0	30	chr	4639675	2811982	2812012	1	30,	0,	2811982,	aactggaagggcttgggatgacacaacagc,	aactggaagggcttgggatgacgcaacagc,
+29	1	0	0	0	0	0	0	+	73_0.500000	30	0	30	chr	4639675	2480740	2480770	1	30,	0,	2480740,	tttaagcgccaaccaggcttctttggttgc,	tttaagcgccaaccaggcttctttagttgc,
+30	0	0	0	0	0	0	0	+	74_0.433333	30	0	30	chr	4639675	1904984	1905014	1	30,	0,	1904984,	acccttctttcgccatatcaaactgatgtc,	acccttctttcgccatatcaaactgatgtc,
+30	0	0	0	0	0	0	0	+	78_0.566667	30	0	30	chr	4639675	4535164	4535194	1	30,	0,	4535164,	cggagtatccgttccccaacgacaagcatc,	cggagtatccgttccccaacgacaagcatc,
+30	0	0	0	0	0	0	0	+	79_0.500000	30	0	30	chr	4639675	3598974	3599004	1	30,	0,	3598974,	aataccgggaagagacaacggggtctcttt,	aataccgggaagagacaacggggtctcttt,
+30	0	0	0	0	0	0	0	-	80_0.500000	30	0	30	chr	4639675	1333814	1333844	1	30,	0,	1333814,	gagaatcagggcttcgcaaccctgtcatta,	gagaatcagggcttcgcaaccctgtcatta,
+30	0	0	0	0	0	0	0	+	82_0.500000	30	0	30	chr	4639675	962544	962574	1	30,	0,	962544,	actgggttgctctgaacaagaaaggcgcta,	actgggttgctctgaacaagaaaggcgcta,
+30	0	0	0	0	0	0	0	+	83_0.533333	30	0	30	chr	4639675	4543338	4543368	1	30,	0,	4543338,	cgccagggacgtatcgcgtcgatatctatt,	cgccagggacgtatcgcgtcgatatctatt,
+30	0	0	0	0	0	0	0	+	86_0.566667	30	0	30	chr	4639675	159366	159396	1	30,	0,	159366,	ggcaacgcaggcgcatgattctgcttggaa,	ggcaacgcaggcgcatgattctgcttggaa,
+29	0	0	1	0	0	0	0	+	87_0.433333	30	0	30	chr	4639675	2137315	2137345	1	30,	0,	2137315,	cgctggatgaaaancgtgaatatcacacca,	cgctggatgaaaaacgtgaatatcacacca,
+30	0	0	0	0	0	0	0	+	88_0.533333	30	0	30	chr	4639675	2263609	2263639	1	30,	0,	2263609,	cgtaccgggctgaaagtagaagagcgtttc,	cgtaccgggctgaaagtagaagagcgtttc,
+30	0	0	0	0	0	0	0	+	90_0.466667	30	0	30	chr	4639675	609915	609945	1	30,	0,	609915,	atcaccgtttcgctaaccggtacgtttaac,	atcaccgtttcgctaaccggtacgtttaac,
+29	1	0	0	0	0	0	0	+	91_0.566667	30	0	30	chr	4639675	2506977	2507007	1	30,	0,	2506977,	ttcgcccggcaagcttacccaacgcttatc,	ttcgcctggcaagcttacccaacgcttatc,
+30	0	0	0	0	0	0	0	+	92_0.533333	30	0	30	chr	4639675	4109771	4109801	1	30,	0,	4109771,	ttttccccgccgttagtagcgactgcagtt,	ttttccccgccgttagtagcgactgcagtt,
+30	0	0	0	0	0	0	0	+	93_0.400000	30	0	30	chr	4639675	2250545	2250575	1	30,	0,	2250545,	ttatttgcccgatgagtcagtttattgcag,	ttatttgcccgatgagtcagtttattgcag,
+30	0	0	0	0	0	0	0	+	94_0.466667	30	0	30	chr	4639675	1274949	1274979	1	30,	0,	1274949,	ccacggtgatatctggtgccatactgataa,	ccacggtgatatctggtgccatactgataa,
+30	0	0	0	0	0	0	0	+	95_0.466667	30	0	30	chr	4639675	3279675	3279705	1	30,	0,	3279675,	tcccccgtaaggcctttctttttctttcgt,	tcccccgtaaggcctttctttttctttcgt,
+30	0	0	0	0	0	0	0	+	97_0.566667	30	0	30	chr	4639675	2779110	2779140	1	30,	0,	2779110,	tgcgccgccggattgttgctcaacatgctt,	tgcgccgccggattgttgctcaacatgctt,
+30	0	0	0	0	0	0	0	+	98_0.366667	30	0	30	chr	4639675	3729759	3729789	1	30,	0,	3729759,	aacgcgctaaccgccaataataacaaaatt,	aacgcgctaaccgccaataataacaaaatt,