bio-ngs 0.3.2.alpha.01

data/spec/fixture/s_1_1_1108_qseq.txt

@@ -0,0 +1,100 @@
+H125	98	1	1108	1586	1989	CGATGT	1	CAGA.C.................A.....GAATGGCATGGATCAAGAAAATCCCCCTTGTGAAGAAGAATCAGCAG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	1879	1986	CGATGT	1	CACA...................C.....GAACCTTTATGAGCCGGCTGCCATCTAGTTTGACGCGGATTCTCTTG	^^^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	1786	1997	CGATGT	1	CGCAGA.T.G.............C.A.TCTGATATGAAACATTGGCCCTTTATGGTGGTGAATGATGCTGGCAGGC	_____\B]B]BBBBBBBBBBBBBTBXBTXZ^]]]^_____`___`__`\`__________^`___Y^^^^`^___B	0
+H125	98	1	1108	2174	1996	CGATGT	1	CTCACA.A...............T.T..ATTCTGTGTTTTATCAAAAAGCAAAGATATTCTCACCTTCACCTTGCT	_^_^_UBSBBBBBBBBBBBBBBBYBRBBUVTYQUT___U^^`^______^_________Y_______\___X___Y	0
+H125	98	1	1108	2322	1999	CGATGT	1	GCTGGG.TTAC...........CC.T.GCCTTAGTTCTTATTTCAAGGAAAAGCTGCTAGAAAGGGAAACCATGAG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	2619	1977	CGATGT	1	CAG...........................CCAGCAGGACACCGCCTGCAGAAAGGACCTGCCCTGATAATGTCCC	]OTBBBBBBBBBBBBBBBBBBBBBBBBBBBXVR[Z_`_____Y__`_____`_____`_`_`________```_Y_	0
+H125	98	1	1108	2850	1986	CGATGT	1	CAAA...................G.....GGTGTGGCCATGAATCCTGTGGAGCATCCTTTTGGAGGTGGCAACCA	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	2828	1997	CGATGT	1	GTGATA.G.T.............C.G.GGCAAGGGGGGTTGGAGGAGCATGAAGCCCCCAATATTATGTAGGTCAC	]_^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	3107	1977	CGATGT	1	CGG...........................GGGCTTAAAAAAAAAAAAAAAAAAAAAACCCATTTTTTTGCTAACG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	3138	1994	CGATGT	1	CTCT.C.T...............A....GCAAAGACAGCAGGCAAGTCATTCTCCAAAGAAAGTGTAAGAGTGCCC	^^^^B[B[BBBBBBBBBBBBBBBTBBBBYZ[][X]______________`____`_____^^`_____\_`__^__	0
+H125	98	1	1108	3326	1979	CGATGT	1	ATT...........................AATGAAAAGATTGCATATAATGCTGCATCTGTTAGAAACAGAACTA	WWWBBBBBBBBBBBBBBBBBBBBBBBBBBBPRVTP____^X`______^_______^_______`\`________S	0
+H125	98	1	1108	3444	1988	CGATGT	1	CGAG...................T.....AGAATTGCATCGTGCTCATCGACAGCACACCGTACCGACAGTGGTAC	Z]]ZBBBBBBBBBBBBBBBBBBB[BBBBBRQWFXT__^____^_`_______^_______^WZ_]^\^^^W^\V__	0
+H125	98	1	1108	3529	1974	CGATGT	1	GTA...........................GCGGACACGGACATGGGT.AA.ACAC.CTGCCTCATGGGGAAACCT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	3620	1995	CGATGT	1	CTCAGA.G...............A....TTCAAGAGGCTAGCCCCAGCCAAGAAGGCCCCCTCAGCCAAGGGGGCA	``___SBYBBBBBBBBBBBBBBBRBBBBXPUWVPU___YYY^^GZOTSXS_Y__YZH[]^^M]YU^``^T^VZVXW	0
+H125	98	1	1108	3845	1975	CGATGT	1	CAC...........................GCTGAAAGCCTAGGGGATGGA.AAGT.GCAGGCAAGCCCCGGGGCG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	4403	1983	CGATGT	1	CTT....................A.....ATGGACATAAACAAACTTTATTGCACACGACTATTGTGAGGATAAAG	]ZWBBBBBBBBBBBBBBBBBBBBPBBBBBPV\VLR_____`_^`^__^__^^___^__Y_`____`_`U`\_____	0
+H125	98	1	1108	4424	1985	CGATGT	1	CCCA...................G.....GTGGTCAGGATCCACTGTGGCTGTGAGTCCCTCCCATCCTGTGGCAC	]X]YBBBBBBBBBBBBBBBBBBBRBBBBBXTW\U[`\______________^Y^\]VY^^__^^N`]_BBBBBBBB	0
+H125	98	1	1108	4718	1991	CGATGT	1	TCCC.T.................T....CAACAACTGAAAACGGATGAGGCCAGACTGACTGAAGGGCCCAAGCCA	^^Z^B[BBBBBBBBBBBBBBBBBRBBBBWWXZSXU______________Y____^_^^^______^____Y__T_Y	0
+H125	98	1	1108	4958	1978	CGATGT	1	GTG...........................ATTAGCCGGGCATGGTAGCGGGCGCCTGTAGTTACAGCTACTCTGG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	4916	1983	CGATGT	1	CCT....................G.....TCCATTTACTTCTTCCCATCCTGGGACCTGCCAGGGCAGCAATCTCT	]][BBBBBBBBBBBBBBBBBBBBRBBBBBRZWWX]_`_______`_______\_______^__\_`____`_`___	0
+H125	98	1	1108	4759	1998	CGATGT	1	CAAAAT.A.A............CC.C.ACATGGGTCTATTTTGTGCTTAAAAATAATTTAAAAATCATACAATATT	``___]B]B]BBBBBBBBBBBBY]B[B[[U\^^^Z_`___`^^^`_``__`___^^[______________\____	0
+H125	98	1	1108	5672	1976	CGATGT	1	AAA...........................AAAAGGACTTTGAAGTTTATCAAGTAGGGAAGAAAAATGTTGCTTT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	5522	1979	CGATGT	1	AGA...........................TCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAACAAATT	VTWBBBBBBBBBBBBBBBBBBBBBBBBBBBXZY[W_Y___^YY^^]ZZW^\_\_\^^`^O^`___^BBBBBBBBBB	0
+H125	98	1	1108	5874	1983	CGATGT	1	CAGC...................A.....TGCGACTGTTTAGTTCTCAGCTCTTTCATCACCTCCTTGCTGGAGAT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	5775	1999	CGATGT	1	GCCTAG.TGCC...........GGAT.AGGATATTTGCTACTTGCAGCCTTTATCAAAATAAGAGACTAGCAAATT	_^^YY[B[UXRBBBBBBBBBBBXZMRBPTPTPQWQW]VVMZ_Z]]Y]_ZU]^\\^]\\Z]^^^U_]]]]__^_^O[	0
+H125	98	1	1108	6560	1978	CGATGT	1	CCA...........................GTCCCCACACCCCATGACACCGCCCGCTCGCCCTCCCTCCATTCTC	]YXBBBBBBBBBBBBBBBBBBBBBBBBBBBXS]YW`_^^___^^__\_______^^_`______`^^^_^^_____	0
+H125	98	1	1108	6500	1978	CGATGT	1	AGA...........................TCACCGATGTATCTCGTATGCCGTATCATTAGATCGGAAGAGCACA	VXUBBBBBBBBBBBBBBBBBBBBBBBBBBBJYUUW_______`___Y___]^^W]____`__YH_^]]\]____\]	0
+H125	98	1	1108	6921	1974	CGATGT	1	AGT...........................AAAATATCAAGGCTCTCA.TG.GAAA.TGTAGACCCCAAATAACTG	][ZBBBBBBBBBBBBBBBBBBBBBBBBBBBX[YXY^`____`^`^^^VBVSBTY]ZB][]^^Y\\_^_____^^__	0
+H125	98	1	1108	7694	1990	CGATGT	1	TAGG.A.................A.....GCTGACAAGGATACTGATAGAAAAAGTGATTTCTTCTTATTATAAAG	][[[BQBBBBBBBBBBBBBBBBBRBBBBBXUWZWZ_^_`________`__^\]]]________^^```_Y_`____	0
+H125	98	1	1108	7856	1988	CGATGT	1	CCCA.T.................T.....CCCTGAGGCCCTCCAGAGGTTATCTGCCCATCATCTCACCATCATGG	^^^^B]BBBBBBBBBBBBBBBBBTBBBBBXVWYUZ_______^^__^__`_\`^^__`_____``_______^__`	0
+H125	98	1	1108	8073	1990	CGATGT	1	GAGG.C.................C.....ACATGCTGCTGGTGATGCTGGAGGACATGAACACAGGGACAGAATCA	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	8108	1993	CGATGT	1	AGCA.T.................G....AAGAAGTCAGAATTTGAAACGGAAGAATGAAGAAAAGAAATAAAAATG	MVRTBPBBBBBBBBBBBBBBBBBOBBBBROTZQUQ^\\\]]^^`U^ZWY^]WW\]YY^V^__^^^^^^^_]XZ]QV	0
+H125	98	1	1108	8747	1974	CGATGT	1	GGA...........................TTTGTAAATAAAATGCTG.CA.GAAA.TTAGAAGGAAAATTAAATT	Z]ZBBBBBBBBBBBBBBBBBBBBBBBBBBBZ]]WX_____`^^^_^X]B]QBRXZWBTZT^VY^^_______``__	0
+H125	98	1	1108	8581	1984	CGATGT	1	GTCA...................G.....GATGAGGAAGATGATCAGGAGGATGATGAAGGTGAAGAGGGAGATGA	][]UBBBBBBBBBBBBBBBBBBBYBBBBBXQRUQU__________^__Y_^X_`^_^^___Y^^^TZRSX`_`^_W	0
+H125	98	1	1108	8516	1990	CGATGT	1	ATTT.G.................T.....TATCAATGCAGCCTTTTCAGCCAATGAGAGGCCTCGTCACCATCACG	VWTXBPBBBBBBBBBBBBBBBBBRBBBBBRTURXW__^\YV]__^_____RPUXV^^\^^U\^\]_____TP]TXS	0
+H125	98	1	1108	8787	1977	CGATGT	1	CAG...........................CTTTCTAGGGACCAGCTGCAGCTCCTTCTCTTGAAGATTGCCACCA	]ZWBBBBBBBBBBBBBBBBBBBBBBBBBBBXV]ZZ_______`____`_^`\___^_\__XZW]Z\]]^\V^TT\^	0
+H125	98	1	1108	8959	1993	CGATGT	1	GGCA.A.................A....TCTCTCTTCTGGTCTTAGCCCACTTAACCCAGTCTGAAGAGCCAAAAT	WTRXBSBBBBBBBBBBBBBBBBBUBBBBXWWZWSWX___Y__\_U[^X[\[[[__^___Y_[]]____W_^Z___\	0
+H125	98	1	1108	8860	1997	CGATGT	1	AAGAAG.T.A.............C.G.TCCACCCATCATCAGCCATCTGAAACTGACAGACTTTGGTCTGTCCCGC	_`___ZBSBZBBBBBBBBBBBBBYBXBY]UY^[[M^_____`________________`__^____________``	0
+H125	98	1	1108	9205	1979	CGATGT	1	GAA...........................GGTGGCGAAGGCCTACGCTGCTCTTGCTGCCCTAGAAAAGCTTTTC	TSOBBBBBBBBBBBBBBBBBBBBBBBBBBBRRQXU_^^Y__\__^_M^V_^]]O]X^_\^`___^W\^W[Y[_TX^	0
+H125	98	1	1108	9076	1982	CGATGT	1	TGG....................G.....ACATGCCTTGGTTCAAGGGATGGAAAGTCACCCGTAAGGATGGCAAT	V\UBBBBBBBBBBBBBBBBBBBBYBBBBBY]X[UU____^__^_______`__`_`^^___``___\_\______U	0
+H125	98	1	1108	9727	1974	CGATGT	1	CAA...........................GCATCACGCCACCTGACT.CA.ACTA.ACTACAAGGCTACAGTAAC	YR[BBBBBBBBBBBBBBBBBBBBBBBBBBBRIZRU__`______`^V\BWZBSMTYB]Z]XVTX]___^___O^__	0
+H125	98	1	1108	9601	1975	CGATGT	1	CAA...........................TATACCAATGACATCATTTCTAGTATATCTTAAAACATTATATTTG	]]VBBBBBBBBBBBBBBBBBBBBBBBBBBBTVW[U`____^_X________`________\`____`^_^_^`___	0
+H125	98	1	1108	9556	1976	CGATGT	1	GAT...........................CACCGATGTCTCTCCTATGCCGTCTTCTTCTTGACAAAAATATGTA	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	9837	1974	CGATGT	1	AAA...........................AACTTCTTCCACAGAGAG.TC.GGGG.CGGAGGGACTCTGCTGAAC	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	10228	1973	CGATGT	1	AGG...........................ATTCTGAAGGGAAAATGG.TC.CTTA.ATTGCAAGTAACCAAAGGA	][]BBBBBBBBBBBBBBBBBBBBBBBBBBBPY\ZX_Y____`___^^]BUZBXZXXBZ[Z^][^]__`__\V]]^^	0
+H125	98	1	1108	10001	1987	CGATGT	1	CGGC...................C.....CCAGAAAGATTATAGTTGTACCCACACCAAGTTCCCATGGTTGAAGC	]]Z]BBBBBBBBBBBBBBBBBBBTBBBBBP]QVLS^^Y^^T]U]V^XXGV^\^]^__________^_`_____`OZ	0
+H125	98	1	1108	10207	1989	CGATGT	1	CTCG.A.................A.....ACTAGTATATCGCTAACACCTCATATCCTCCCTACTATGCCAAGAAG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	10270	1999	CGATGT	1	GATTCA.ACAC...........TTCCTAACCAGCAAGGCCCCCATACACCATCTATTCCATAAACCACTCAGGTTA	_____]B^]]RBBBBBBBBBBBRYV[ZY][__Y___Y_OY_____TY^YU__\____________^____\U]]\Z	0
+H125	98	1	1108	10617	1987	CGATGT	1	CCAG...................G.....TCTGGATTTTCTTTCTGCCTCTTCTATCCAGAAAGGATACTGGAGAA	]][YBBBBBBBBBBBBBBBBBBBTBBBBBR[T\U[`___^^^`^^_______`_____\__`________Y_____	0
+H125	98	1	1108	10985	1979	CGATGT	1	CCA...........................CTGGAAGTCCTAGCCAAAGCAATCAGACAAGAGAAAGAAATAAAGG	TY[BBBBBBBBBBBBBBBBBBBBBBBBBBBYWWYZ_`_^___^Y_\^___`_V__^__^_^^^O^S^[[]^_X^^\	0
+H125	98	1	1108	10934	1987	CGATGT	1	CTTT...................T.....CCAAGATGATGCTTGGTGCTCTAGCCATCACTTCCTGGCCTGCAGGG	]URQBBBBBBBBBBBBBBBBBBBVBBBBBRTXYRU________V_Z]ZJ^\]Z]^______\________^Y_Y__	0
+H125	98	1	1108	11197	1979	CGATGT	1	TTG...........................AAAAGGCCTGCGACCATGTCTGCCACCCAACCATTTATTTTCTACT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	11485	1976	CGATGT	1	TGT...........................AGGAACGCAGACACATTCAGATGCCTTTGCAGAAAGAGATGCCAGA	][ZBBBBBBBBBBBBBBBBBBBBBBBBBBBP\YXV____^__`^_____\_______^__``^_^________^\_	0
+H125	98	1	1108	11450	1977	CGATGT	1	CCT...........................GATGCCAAACGGTGGAGCCTTGAAGATACATTTCCTCTCCTTCTGT	]VVBBBBBBBBBBBBBBBBBBBBBBBBBBBXPSNN_______^_VZZ]]]_`__^\_`___`______^___`W_^	0
+H125	98	1	1108	11381	1997	CGATGT	1	ATCCAT.C.T............GC.T.CATCCACCCATCCAGCCATGCACCTGCCCATCCATCAATTCACTGATCC	_`__`ZB]B]BBBBBBBBBBBBXRBZBZ[W_`_[^^^^_`___`_______^_\`_______`__`_______^`_	0
+H125	98	1	1108	11507	1973	CGATGT	1	GGA...........................AGGAGACTAGCACAGGGA.TT.TCCT.ATCCTCACCATCACACCTG	W[[BBBBBBBBBBBBBBBBBBBBBBBBBBBRXXZQ`^___Y____^X\B\QBPZXOBTVW\X^\^_`VY_Y]^XOY	0
+H125	98	1	1108	12016	1998	CGATGT	1	CCACTC.G.AG...........CC.G.CTGTGGTGATGCCTCAGTTTGGACAGAAACTCAAACCTGACGCACAAAC	__``_[B]BRXBBBBBBBBBBBQZB]BURXYY^^^_`_______`___________`____`__\_`_\_^_\__^	0
+H125	98	1	1108	12414	1984	CGATGT	1	GTTT...................T.....ACTTATAAGGCTGCAGTCTAGGAGGCAGAGCAATGAATCATTACAAT	]VWZBBBBBBBBBBBBBBBBBBB[BBBBBUVRZOX_________`_____`_______\_Y______`______`_	0
+H125	98	1	1108	12441	1993	CGATGT	1	CAGC.G.T...............T....TAGAATCAGGTCTATTGCACGTCTGGCCAATATTGATGAAGAAATGCT	]U[YBTBYBBBBBBBBBBBBBBBTBBBBPLTSUZP_^___\Y^^^______`_`_`_U________`___U^^___	0
+H125	98	1	1108	12850	1984	CGATGT	1	CGGG...................T.....TCCCAAGTAGCTGGAATTACAAGCGTGTGCCACCAAGCCTGGCTAAT	]ZZ]BBBBBBBBBBBBBBBBBBBRBBBBBQWPNPQ__`_^____YYZY^TW^T\T]Z\]Z___________^^_^V	0
+H125	98	1	1108	12905	1989	CGATGT	1	GGCC.C.................T.....CGCGGCCGGCGCGCACCTTCGTGTGGTACTGAAACGAGGGGCAGCCC	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	12929	1991	CGATGT	1	AGAT.G.................A....AGTCACCGATGTATCTCGTATGCCGTATCATTAGATCGGAAGAGCACA	YZ[YBSBBBBBBBBBBBBBBBBBXBBBBPZSW[XW_^``_______^__`______^_V_VR\\[\__^]V_^__`	0
+H125	98	1	1108	13719	1980	CGATGT	1	GCG....................T......GGGGACCTTCGGCCGAGTTGTACAATGTGTTGACCATCGCAGGGGT	]]]BBBBBBBBBBBBBBBBBBBBYBBBBBBX[T[U_`__________________`_`___\__``Y___VY_\^V	0
+H125	98	1	1108	13548	1995	CGATGT	1	CCGGCC.C...............T.G..ATAAAGTCTTGCTTTGTTACCCAGATTGGCCTGAAACTCCTGAGCTCA	___Y`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	13959	1988	CGATGT	1	TCAA.G.................T.....TCATTCACGAAATAAATACAGTGATCATTCACAGTGTAGTAGATCAT	]XWSBVBBBBBBBBBBBBBBBBBXBBBBBT[TT[VY_^_____^V`__`____\\\_____\_`_^`_^___^__`	0
+H125	98	1	1108	14218	1997	CGATGT	1	TGGGCA.G.A............CA.A.TTGCTATCTGTATACACGTTTTTTCTTTTTTCCTTTCCCAGTTCTAAGG	_____ZB]BZBBBBBBBBBBBBXYBZBZ[Z_`^`^_`__\____`_____``^`^`^^`___`_______`__Y_]	0
+H125	98	1	1108	14318	1979	CGATGT	1	GAC...........................AAAGAAAAAAAAGACAAAAGAAGAAAAGGAGCTACCATGCAGTCCA	]XWBBBBBBBBBBBBBBBBBBBBBBBBBBBWVTQR^^^^S^^^^^^__^XPX[V^^^X`_O____^`__YRHT[S_	0
+H125	98	1	1108	14432	1988	CGATGT	1	AGCA.T.................C.....CTTCTAAGTTATATAAACACTTTTAATGCAAACATTCAATAGGGCAT	^^^^B]BBBBBBBBBBBBBBBBBWBBBBBX[X[ZZ__`__`__`_______`__________________`_____	0
+H125	98	1	1108	14609	1991	CGATGT	1	AGAA.A.................A....GTGGGATATATTAAAAGCACCTTGGGAGGCTGAGGCGGGCAGATCACG	][[YBXBBBBBBBBBBBBBBBBBRBBBBXXZZYYZ_^______`^__`________^^____^___^^`^_\`___	0
+H125	98	1	1108	14813	1974	CGATGT	1	AGA...........................TCACCGATGTATCTCGTA.GC.GTCT.CTGCTTGAAAAAACATCCA	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	15180	1989	CGATGT	1	ATTT.G.................C.....TCAATGACACTTTTGTCCATGTCACTGATCTTTCTGGCAAGGAAACC	]Z[[BZBBBBBBBBBBBBBBBBBYBBBBBPTTTZT^_____`__^^___^_^\\____^___`__^\_V\V_\^]Y	0
+H125	98	1	1108	15469	1989	CGATGT	1	ACTG.A.................G.....GCGTCTTCAGAGGGGGGTAGCATGACCTCAAGCCTTCTATAAAAGCC	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	15599	1981	CGATGT	1	GCT....................A.....CACTAGGTCTCCTCTGGCACCCATGTGTGGGAATGTGAGTGCCTTGT	]YYBBBBBBBBBBBBBBBBBBBBVBBBBBXZUZWV_________________`______^V________`__^`__	0
+H125	98	1	1108	15785	1987	CGATGT	1	CGCA...................G.....GAGTAGCAGCTCCCGCTGGTGTGCGGCTAGGGGTAGGATCCCATATT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	16225	1978	CGATGT	1	CTG...........................GCGGAGTCTCTTCCCTTGCGTGCATAGGTCCCGGTTGGTAGAGGGT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	16515	1977	CGATGT	1	CAG...........................TCAATACGGGGAAAAATAAAGTGAGGCGAGTGAAGACCATTTATGC	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	16914	1985	CGATGT	1	AGAT...................A.....GTCACCGATGTATCTCGTATGCCGTCTTCTGCTTGAAAAAAACAACA	]]]]BBBBBBBBBBBBBBBBBBBZBBBBBTRX\[Z__`__^UU^^___Y__`__`_`_UI^`BBBBBBBBBBBBBB	0
+H125	98	1	1108	17210	1978	CGATGT	1	CCC...........................TGTACCTTCCTGAGCTGAGACATGAGCCACACCTGGGTCCATGTGA	]]]BBBBBBBBBBBBBBBBBBBBBBBBBBBXQMNQ__^_____T__Y______^___YI^WW^^Z_PZZ___^_\]	0
+H125	98	1	1108	17560	1987	CGATGT	1	CACG.G.................C.....CGCGCCCACCCCCCCCCGCCGGGCCCGCACGGGGAGTCACCACCTTG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	17716	1987	CGATGT	1	TGGG.G.................T.....GGCTGAGACCGGAGAATCCCTTGAACCCAGGAGGCAGAGGCTGCAGT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	17756	1977	CGATGT	1	CTG...........................TCGTGCCATTGCACTCCATCTTGGGTGACAGAGTGAGACATCATCT	Z]ZBBBBBBBBBBBBBBBBBBBBBBBBBBBNQQKZ____Y__^_^________^_______^`__`\__^^_Y__^	0
+H125	98	1	1108	17851	1988	CGATGT	1	CAGA.C.................T.....TAAAAGCCAAAATGGGAAAGGAAAAGACTCATATCAACATTGTCGTC	][][BZBBBBBBBBBBBBBBBBBYBBBBBRZPZNZ__\__^`__^___`_\_\^^^^__\_`^_Y__________\	0
+H125	98	1	1108	18055	1974	CGATGT	1	GTT...........................CTATAGGAGTGGATGATG.AG.TATT.GTCATTGCATGATAGGATA	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	18193	1990	CGATGT	1	CTTA.C.................A....AGGGAGCCTCTGGGGTTAGGATCAGTAAGGTTTGCTGTCGTTTTTGGA	]Z]ZBQBBBBBBBBBBBBBBBBBRBBBBRQWWU[W__Y___________Y_\^_\_____U`__^\^_]\O^^^^V	0
+H125	98	1	1108	18377	1977	CGATGT	1	GGC...........................CAAATATAAGGAAATGGCCCAATGAACGTGGTTGTGGGAGGGGAAA	WZWBBBBBBBBBBBBBBBBBBBBBBBBBBBRUVLU_`__`__________________\_`_`^___\`_^^^^BB	0
+H125	98	1	1108	18485	1979	CGATGT	1	ATA...........................CGAGATGAGCTCAGATCTACCTTTCCTCTTCATGGACCAGACTGGA	VQQBBBBBBBBBBBBBBBBBBBBBBBBBBBRQVWU___`_V`^VXYL^^Z[RW^WI^\^U]]]Y]________`QV	0
+H125	98	1	1108	18436	1988	CGATGT	1	CTTA.A.................A.....CTGTTTGGCTTCAACTCCTACTTTTTTCAGCACGATTCCTTTTGCAT	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	18330	1992	CGATGT	1	CTTT.A.................T....GTAAAAGGAGAAAAAGATGCGGGGGAAATGGAGCAGGGGGTGGGGAAA	][U[BWBBBBBBBBBBBBBBBBBRBBBBSOSWJWW_V_Y_^ZXZZSNZ^O_`^^__Y__NY^^\YZ]^VVX\YWXV	0
+H125	98	1	1108	19283	1973	CGATGT	1	CTT...........................CACAGCCTGTTTAATCTG.TG.TTGT.GGCTTTAACATCCACAATG	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	19389	1994	CGATGT	1	TGCT.A.C...............A....TGAGACCAGTTCACTAGAAGAAACAAACATTTCTGCCATGCAGACCAA	^^^^B]B]BBBBBBBBBBBBBBBVBBBBT[W]ZZX_`______`^___`_^^_^^^_`__________^_\_____	0
+H125	98	1	1108	19966	1977	CGATGT	1	CCT...........................GGAAAACATGTCTTCAGAAATAAATGCTTCCTCTTCCAGGTAGTTC	]RYBBBBBBBBBBBBBBBBBBBBBBBBBBBRUMVS__^^________^__\]]`]___^`^_`____^__Z^\Z^`	0
+H125	98	1	1108	20041	1984	CGATGT	1	CTTT...................G.....GAGGTGCAGGGGGCGCAGGGGGCGGCGTCACCGAGGAGCAGGCGGGC	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	20230	2000	CGATGT	1	GTGAAG.ATATA....G.....TATTCTCCCCCAGTTTGGCAGAGGCTGGCCCTCTTTTGACTGCCCCTGCTTTCT	_____\B\^VOQBBBBXBBBBBHOUUMZR[]]XX]___Y^__Y\X^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	20276	1979	CGATGT	1	TCT....................G......GGCGCACATAGACTACTCCAGGAGTAAGTTGTTCTTGTTTTTTTCG	VYPBBBBBBBBBBBBBBBBBBBBTBBBBBBYWSTRX\^]]____Y]W]TKUYOSLS[ZXXUV^W^]XT^]^`^^^_	0
+H125	98	1	1108	20743	1977	CGATGT	1	CTG...........................TTGACAGAGCCAACTCCCTTGAGGGTGGCAGGAAGCACACCCCCCA	BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	20532	1980	CGATGT	1	CTA....................A.....TTTTGGTAGAGATGGGGATTTTGCCATGTTGCCCAGGCTGGTCTCCT	]VRBBBBBBBBBBBBBBBBBBBBRBBBBBP]SRR]_______`______^________`\___X___`_^SRP\\^	0
+H125	98	1	1108	20881	1975	CGATGT	1	CTC...........................ATCAATCATATACAGAATATCTACAAAAAACCTACATCATACTTAA	]X]BBBBBBBBBBBBBBBBBBBBBBBBBBBXVSUN__U__`____^X^V\^]\_]_`^XX^`\_`_`___^_Y`^_	0
+H125	98	1	1108	21009	2000	CGATGT	1	GTGGCG.CGGGT....G.....GGGTCGAAGTCAAGGCCCTGGCTTGACGCTGGTGCCACCGCGAACGCTCGCACA	_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB	0
+H125	98	1	1108	1188	2036	CGATGT	1	CTTGTATGCAGCATCCCCTTCTTGCCTAGGGACTTGAAGGGCCAGGCTTCCTGTCATTGCCTCACTCAAATGTAGC	gggggggggggggegggggffggeggegggeagge^ggdbcgggcdgedegfggffff^ffffefdeeZefccceg	1
+H125	98	1	1108	1147	2046	CGATGT	1	CGGGAAATGGCGGAAATGTGCAAGGATGTTATATGAATTGTGTTGGTTGGCCTAAAACACAGAGCCGGCTTGAAGT	[XSZGXPSKPJPP]TWQRFRHXW\WXXX]PUX[W_^R^[XRNRYV]^Y[]UUNRT]X_BBBBBBBBBBBBBBBBBB	0

data/spec/quality_spec.rb

@@ -0,0 +1,40 @@
+#
+#  tophat_spec.rb - RSpec Test
+#
+# Copyright:: Copyright (C) 2011
+#     Raoul Bonnal <r@bioruby.org>
+# License:: The Ruby License
+#
+#
+
+
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "When quality is read" do
+  it "should give me back the quality scores of first read in Illumina 1.5+ encoding" do
+    read = Bio::FlatFile.auto(File.dirname(__FILE__) + "/fixture/test.fastq").first
+    read.format = :fastq_illumina
+    qual = read.quality_scores
+    qual.should == [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 37, 39, 39, 39, 39, 39, 38, 38, 39, 39, 37, 39, 39, 37, 39, 39, 39, 37, 33, 39, 39, 37, 30, 39, 39, 36, 34, 35, 39, 39, 39, 35, 36, 39, 37, 36, 37, 39, 38, 39, 39, 38, 38, 38, 38, 30, 38, 38, 38, 38, 37, 38, 36, 37, 37, 26, 37, 38, 35, 35, 35, 37, 39]
+  end
+
+  it "should give me back the quality scores of last read, with Bs in Illumina 1.5+ encoding" do
+    quals = []
+    Bio::FlatFile.auto(File.dirname(__FILE__) + "/fixture/test.fastq").each do |read|
+      read.format = :fastq_illumina
+      quals = read.quality_scores
+    end
+    quals.should == [27, 24, 19, 26, 7, 24, 16, 19, 11, 16, 10, 16, 16, 29, 20, 23, 17, 18, 6, 18, 8, 24, 23, 28, 23, 24, 24, 24, 29, 16, 21, 24, 27, 23, 31, 30, 18, 30, 27, 24, 18, 14, 18, 25, 22, 29, 30, 25, 27, 29, 21, 21, 14, 18, 20, 29, 24, 31, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
+  end
+
+  it "should tell me how many B are in the sequence with Illumina 1.5+ encoding" do
+    reads = Bio::Ngs::FastQuality.new(File.dirname(__FILE__) + "/fixture/test.fastq")
+    reads.quality_profile.should == nil
+  end
+  
+  it "should return the comulative count of Bs in all the sequences" do
+    reads = Bio::Ngs::FastQuality.new(File.dirname(__FILE__) + "/fixture/test.fastq", :fastq_illumina)
+#    reads = Bio::Ngs::FastQuality.new("/Users/bonnalraoul/Desktop/s_1_1_1108_qseq.fastq", :fastq_illumina)
+    reads.track_b_count.b_profile.should == [[58, 1], [59, 1], [60, 1], [61, 1], [62, 1], [63, 1], [64, 1], [65, 1], [66, 1], [67, 1], [68, 1], [69, 1], [70, 1], [71, 1], [72, 1], [73, 1], [74, 1], [75, 1]]
+  end
+end

data/spec/sff_extract_spec.rb

@@ -0,0 +1,98 @@
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+require 'thor/base'
+
+describe "SffExtract" do
+  
+  describe "class" do
+    it "should have default options" do
+      Bio::Ngs::SffExtract.options.should == {"append" => {:type => :boolean, :aliases => "-a", :desc =>"append output to existing files"},
+                                              "xml_info" => {:type => :string, :aliases => "-i", :desc => "extra info to write in the xml file"},
+                                              "linker_file" => {:type => :string, :aliases => "-l", :desc => "FASTA file with paired-end linker sequences"},
+                                              "clip" => {:type => :boolean, :aliases => "-c", :desc => "clip (completely remove) ends with low qual and/or adaptor sequence"},
+                                              "upper_case" => {:type => :boolean, :aliases => "-u", :desc => "all bases in upper case, including clipped ends"},
+                                              "min_left_clip" => {:type => :numeric, :desc => "if the left clip coming from the SFF is smaller than this value, override it"},
+                                              "fastq" => {:type => :boolean, :aliases => "-Q", :desc => "store as FASTQ file instead of FASTA + FASTA quality file"},
+                                              "out_basename" => {:type => :string, :aliases => "-o", :desc => "base name for all output files"},
+                                              "seq_file" => {:type => :string, :aliases => "-s", :desc => "output sequence file name"},
+                                              "qual_file" => {:type => :string, :aliases => "-q", :desc => "output quality file name"},
+                                              "xml_file" => {:type => :string, :aliases => "-x", :desc => "output ancillary xml file name"}
+                                              }
+    end
+    it "should have a default program name" do
+      Bio::Ngs::SffExtract.program.should == Bio::Ngs::Utils.binary("sff_extract")
+    end
+    
+  end
+  
+  describe "instance" do
+    it "has default options" do
+      Bio::Ngs::SffExtract.new.options.should == {"append" => {:type => :boolean, :aliases => "-a", :desc =>"append output to existing files"},
+                                              "xml_info" => {:type => :string, :aliases => "-i", :desc => "extra info to write in the xml file"},
+                                              "linker_file" => {:type => :string, :aliases => "-l", :desc => "FASTA file with paired-end linker sequences"},
+                                              "clip" => {:type => :boolean, :aliases => "-c", :desc => "clip (completely remove) ends with low qual and/or adaptor sequence"},
+                                              "upper_case" => {:type => :boolean, :aliases => "-u", :desc => "all bases in upper case, including clipped ends"},
+                                              "min_left_clip" => {:type => :numeric, :desc => "if the left clip coming from the SFF is smaller than this value, override it"},
+                                              "fastq" => {:type => :boolean, :aliases => "-Q", :desc => "store as FASTQ file instead of FASTA + FASTA quality file"},
+                                              "out_basename" => {:type => :string, :aliases => "-o", :desc => "base name for all output files"},
+                                              "seq_file" => {:type => :string, :aliases => "-s", :desc => "output sequence file name"},
+                                              "qual_file" => {:type => :string, :aliases => "-q", :desc => "output quality file name"},
+                                              "xml_file" => {:type => :string, :aliases => "-x", :desc => "output ancillary xml file name"}
+                                              }
+    end
+    
+    it "has custom name" do
+      Bio::Ngs::SffExtract.new("/usr/local/bin/sff_extract").program.should == "/usr/local/bin/sff_extract"
+    end
+    
+    it "overwrites specifc option" do
+      tophat = Bio::Ngs::SffExtract.new
+      tophat.options={:reads=>{:type=>:numeric}}
+      tophat.options[:reads][:type].should == :numeric
+    end
+  
+    it "add custom option" do
+      tophat = Bio::Ngs::SffExtract.new
+      tophat.options={:parameter_xxx=>{:type=>:numeric}}
+      tophat.options.should == {"append" => {:type => :boolean, :aliases => "-a", :desc =>"append output to existing files"},
+                                              "xml_info" => {:type => :string, :aliases => "-i", :desc => "extra info to write in the xml file"},
+                                              "linker_file" => {:type => :string, :aliases => "-l", :desc => "FASTA file with paired-end linker sequences"},
+                                              "clip" => {:type => :boolean, :aliases => "-c", :desc => "clip (completely remove) ends with low qual and/or adaptor sequence"},
+                                              "upper_case" => {:type => :boolean, :aliases => "-u", :desc => "all bases in upper case, including clipped ends"},
+                                              "min_left_clip" => {:type => :numeric, :desc => "if the left clip coming from the SFF is smaller than this value, override it"},
+                                              "fastq" => {:type => :boolean, :aliases => "-Q", :desc => "store as FASTQ file instead of FASTA + FASTA quality file"},
+                                              "out_basename" => {:type => :string, :aliases => "-o", :desc => "base name for all output files"},
+                                              "seq_file" => {:type => :string, :aliases => "-s", :desc => "output sequence file name"},
+                                              "qual_file" => {:type => :string, :aliases => "-q", :desc => "output quality file name"},
+                                              "xml_file" => {:type => :string, :aliases => "-x", :desc => "output ancillary xml file name"},
+                                              :parameter_xxx=>{:type=>:numeric}
+                                              }
+    end
+    
+    it "set a default option to be returned as params" do
+      tophat = Bio::Ngs::SffExtract.new
+      tophat.options={:parameter_xxx=>{:type=>:numeric, :default=>10}}
+      tophat.params.should == {:parameter_xxx=>{:type=>:numeric, :default=>10}}
+    end
+
+    it "get normalized options" do
+      tophat = Bio::Ngs::SffExtract.new
+      tophat.options={:parameter_xxx=>{:type=>:numeric, :default=>10}}
+      tophat.normalize_params.should == "--parameter_xxx=10"
+    end
+
+    it "does not save a valid parameter/option" do
+      tophat = Bio::Ngs::SffExtract.new
+      tophat.params={:fake_parameter=>1234567890}
+      tophat.normalize_params.should == []
+    end
+
+    it "set a default option and get the parameters for the binary program" do
+      tophat = Bio::Ngs::SffExtract.new
+      tophat.options={:parameter_xxx=>{:type=>:numeric, :default=>10}}
+      tophat.params={:fake_parameter=>01}
+      tophat.normalize_params.should == "--parameter_xxx=10"
+    end
+    
+  end
+  
+end

data/spec/spec_helper.rb

@@ -0,0 +1,55 @@
+$TESTING=true
+
+# require 'simplecov'
+# SimpleCov.start do
+#   add_group 'Libraries', 'lib'
+#   add_group 'Specs', 'spec'
+# end
+
+require 'thor'
+require 'thor/base'
+require 'stringio'
+require 'rdoc'
+require 'rspec'
+require 'diff/lcs' # You need diff/lcs installed to run specs (but not to run Thor).
+#require 'fakeweb'  # You need fakeweb installed to run specs (but not to run Thor).
+
+$:.unshift(File.join(File.dirname(__FILE__), "..", "lib"))
+
+require 'bio-ngs'
+
+# Set shell to basic
+$0 = "thor"
+$thor_runner = true
+ARGV.clear
+Thor::Base.shell = Thor::Shell::Basic
+
+# Load fixtures
+%w(bwa history project quality rna sff_extract).each do |task|
+  load File.join(File.dirname(__FILE__), "..", "lib", "tasks", "#{task}.thor" )
+end
+
+RSpec.configure do |config|
+  def capture(stream)
+    begin
+      stream = stream.to_s
+      eval "$#{stream} = StringIO.new"
+      yield
+      result = eval("$#{stream}").string
+    ensure
+      eval("$#{stream} = #{stream.upcase}")
+    end
+
+    result
+  end
+
+  def source_root
+    File.join(File.dirname(__FILE__), "..", "lib", "tasks")
+  end
+
+  def destination_root
+    File.join(File.dirname(__FILE__), 'sandbox')
+  end
+
+  alias :silence :capture
+end

data/spec/tophat_spec.rb

@@ -0,0 +1,99 @@
+#
+#  tophat_spec.rb - RSpec Test
+#
+# Copyright:: Copyright (C) 2011
+#     Raoul Bonnal <r@bioruby.org>
+# License:: The Ruby License
+#
+#
+
+
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Tophat" do 
+  describe "class" do
+    it "default options" do
+      Bio::Ngs::Tophat.options.should == {"output-dir"=>{:type=>:string, :aliases=>"-o"}, "min-anchor"=>{:type=>:numeric, :aliases=>"-a"}, "splice-mismatches"=>{:type=>:numeric, :aliases=>"-m"}, "min-intron"=>{:type=>:numeric, :aliases=>"-i"}, "max-intront"=>{:type=>:numeric, :aliases=>"-I"}, "max-multihits"=>{:type=>:numeric, :aliases=>"-g"}, "min-isoform_fraction"=>{:type=>:numeric, :aliases=>"-F"}, "solexa-quals"=>{:type=>:boolean}, "solexa1.3-quals"=>{:type=>:boolean, :aliases=>"--phred64-quals"}, :quals=>{:type=>:boolean, :aliases=>"-Q"}, "integer-quals"=>{:type=>:boolean}, :color=>{:type=>:boolean, :aliases=>"-C"}, "library-type"=>{:type=>:string}, "num-threads"=>{:type=>:numeric, :aliases=>"-p"}, "GTF"=>{:type=>:string, :aliases=>"-G"}, "raw-juncs"=>{:type=>:string, :aliases=>"-j"}, :insertions=>{:type=>:string}, :deletions=>{:type=>:string}, "mate-inner-dist"=>{:type=>:numeric, :aliases=>"-r"}, "mate-std-dev"=>{:type=>:numeric}, "no-novel-juncs"=>{:type=>:boolean}, "no-gtf-juncs"=>{:type=>:boolean}, "no-coverage-search"=>{:type=>:boolean}, "coverage-search"=>{:type=>:boolean}, "no-closure-search"=>{:type=>:boolean}, "closure-search"=>{:type=>:boolean}, "fill-gaps"=>{:type=>:boolean}, "microexon-search"=>{:type=>:boolean}, "butterfly-search"=>{:type=>:boolean}, "no-butterfly-search"=>{:type=>:boolean}, "keep-tmp"=>{:type=>:boolean}, "tmp-dir"=>{:type=>:string}, "segment-mismatches"=>{:type=>:numeric}, "segment-length"=>{:type=>:numeric}, "min-closure-exon"=>{:type=>:numeric}, "min-closure-intron"=>{:type=>:numeric}, "max-closure-intron"=>{:type=>:numeric}, "min-coverage-intron"=>{:type=>:numeric}, "max-coverage-intron"=>{:type=>:numeric}, "min-segment-intron"=>{:type=>:numeric}, "max-segment-intron"=>{:type=>:numeric}, "rg-id"=>{:type=>:string}, "rg-sample"=>{:type=>:string}, "rg-library"=>{:type=>:string}, "rg-description"=>{:type=>:string}, "rg-platform-unit"=>{:type=>:string}, "rg-center"=>{:type=>:string}, "rg-date"=>{:type=>:string}, "rg-platform"=>{:type=>:string}}     
+    end
+    
+    it "has default program name" do
+      Bio::Ngs::Tophat.program.should == Bio::Ngs::Utils.binary("tophat/tophat")
+    end
+  end
+  
+  describe "instance" do
+    it "has default options" do
+      Bio::Ngs::Tophat.new.options.should == {"output-dir"=>{:type=>:string, :aliases=>"-o"}, "min-anchor"=>{:type=>:numeric, :aliases=>"-a"}, "splice-mismatches"=>{:type=>:numeric, :aliases=>"-m"}, "min-intron"=>{:type=>:numeric, :aliases=>"-i"}, "max-intront"=>{:type=>:numeric, :aliases=>"-I"}, "max-multihits"=>{:type=>:numeric, :aliases=>"-g"}, "min-isoform_fraction"=>{:type=>:numeric, :aliases=>"-F"}, "solexa-quals"=>{:type=>:boolean}, "solexa1.3-quals"=>{:type=>:boolean, :aliases=>"--phred64-quals"}, :quals=>{:type=>:boolean, :aliases=>"-Q"}, "integer-quals"=>{:type=>:boolean}, :color=>{:type=>:boolean, :aliases=>"-C"}, "library-type"=>{:type=>:string}, "num-threads"=>{:type=>:numeric, :aliases=>"-p"}, "GTF"=>{:type=>:string, :aliases=>"-G"}, "raw-juncs"=>{:type=>:string, :aliases=>"-j"}, :insertions=>{:type=>:string}, :deletions=>{:type=>:string}, "mate-inner-dist"=>{:type=>:numeric, :aliases=>"-r"}, "mate-std-dev"=>{:type=>:numeric}, "no-novel-juncs"=>{:type=>:boolean}, "no-gtf-juncs"=>{:type=>:boolean}, "no-coverage-search"=>{:type=>:boolean}, "coverage-search"=>{:type=>:boolean}, "no-closure-search"=>{:type=>:boolean}, "closure-search"=>{:type=>:boolean}, "fill-gaps"=>{:type=>:boolean}, "microexon-search"=>{:type=>:boolean}, "butterfly-search"=>{:type=>:boolean}, "no-butterfly-search"=>{:type=>:boolean}, "keep-tmp"=>{:type=>:boolean}, "tmp-dir"=>{:type=>:string}, "segment-mismatches"=>{:type=>:numeric}, "segment-length"=>{:type=>:numeric}, "min-closure-exon"=>{:type=>:numeric}, "min-closure-intron"=>{:type=>:numeric}, "max-closure-intron"=>{:type=>:numeric}, "min-coverage-intron"=>{:type=>:numeric}, "max-coverage-intron"=>{:type=>:numeric}, "min-segment-intron"=>{:type=>:numeric}, "max-segment-intron"=>{:type=>:numeric}, "rg-id"=>{:type=>:string}, "rg-sample"=>{:type=>:string}, "rg-library"=>{:type=>:string}, "rg-description"=>{:type=>:string}, "rg-platform-unit"=>{:type=>:string}, "rg-center"=>{:type=>:string}, "rg-date"=>{:type=>:string}, "rg-platform"=>{:type=>:string}}
+    end
+    
+    it "has custom name" do
+      Bio::Ngs::Tophat.new("/usr/local/bin/tophat").program.should == "/usr/local/bin/tophat"
+    end
+    
+    it "overwrites specifc option" do
+      tophat = Bio::Ngs::Tophat.new
+      tophat.options={:reads=>{:type=>:numeric}}
+      tophat.options[:reads][:type].should == :numeric
+    end
+  
+    it "add custom option" do
+      tophat = Bio::Ngs::Tophat.new
+      tophat.options={:parameter_xxx=>{:type=>:numeric}}
+      tophat.options.should == {"output-dir"=>{:type=>:string, :aliases=>"-o"}, "min-anchor"=>{:type=>:numeric, :aliases=>"-a"}, "splice-mismatches"=>{:type=>:numeric, :aliases=>"-m"}, "min-intron"=>{:type=>:numeric, :aliases=>"-i"}, "max-intront"=>{:type=>:numeric, :aliases=>"-I"}, "max-multihits"=>{:type=>:numeric, :aliases=>"-g"}, "min-isoform_fraction"=>{:type=>:numeric, :aliases=>"-F"}, "solexa-quals"=>{:type=>:boolean}, "solexa1.3-quals"=>{:type=>:boolean, :aliases=>"--phred64-quals"}, :quals=>{:type=>:boolean, :aliases=>"-Q"}, "integer-quals"=>{:type=>:boolean}, :color=>{:type=>:boolean, :aliases=>"-C"}, "library-type"=>{:type=>:string}, "num-threads"=>{:type=>:numeric, :aliases=>"-p"}, "GTF"=>{:type=>:string, :aliases=>"-G"}, "raw-juncs"=>{:type=>:string, :aliases=>"-j"}, :insertions=>{:type=>:string}, :deletions=>{:type=>:string}, "mate-inner-dist"=>{:type=>:numeric, :aliases=>"-r"}, "mate-std-dev"=>{:type=>:numeric}, "no-novel-juncs"=>{:type=>:boolean}, "no-gtf-juncs"=>{:type=>:boolean}, "no-coverage-search"=>{:type=>:boolean}, "coverage-search"=>{:type=>:boolean}, "no-closure-search"=>{:type=>:boolean}, "closure-search"=>{:type=>:boolean}, "fill-gaps"=>{:type=>:boolean}, "microexon-search"=>{:type=>:boolean}, "butterfly-search"=>{:type=>:boolean}, "no-butterfly-search"=>{:type=>:boolean}, "keep-tmp"=>{:type=>:boolean}, "tmp-dir"=>{:type=>:string}, "segment-mismatches"=>{:type=>:numeric}, "segment-length"=>{:type=>:numeric}, "min-closure-exon"=>{:type=>:numeric}, "min-closure-intron"=>{:type=>:numeric}, "max-closure-intron"=>{:type=>:numeric}, "min-coverage-intron"=>{:type=>:numeric}, "max-coverage-intron"=>{:type=>:numeric}, "min-segment-intron"=>{:type=>:numeric}, "max-segment-intron"=>{:type=>:numeric}, "rg-id"=>{:type=>:string}, "rg-sample"=>{:type=>:string}, "rg-library"=>{:type=>:string}, "rg-description"=>{:type=>:string}, "rg-platform-unit"=>{:type=>:string}, "rg-center"=>{:type=>:string}, "rg-date"=>{:type=>:string}, "rg-platform"=>{:type=>:string}, :parameter_xxx=>{:type=>:numeric}}
+    end
+    
+    it "set a default option to be returned as params" do
+      tophat = Bio::Ngs::Tophat.new
+      #setting a default options
+      #TODO: add check between type and default value, in the main class,
+      # Thor already does it.
+      tophat.options={:parameter_xxx=>{:type=>:numeric, :default=>10}}
+      tophat.params.should == {:parameter_xxx=>{:type=>:numeric, :default=>10}}
+    end
+
+    it "get normalized options" do
+      tophat = Bio::Ngs::Tophat.new
+      #setting a default options
+      #TODO: add check between type and default value, in the main class,
+      # Thor already does it.
+      tophat.options={:parameter_xxx=>{:type=>:numeric, :default=>10}}
+      tophat.normalize_params.should == "--parameter_xxx=10"
+    end
+
+    it "does not save a valid parameter/option" do
+      tophat = Bio::Ngs::Tophat.new
+      tophat.params={:fake_parameter=>1234567890}
+      tophat.normalize_params.should == []
+    end
+
+    it "set a default option and get the parameters for the binary program" do
+      tophat = Bio::Ngs::Tophat.new
+      #setting a default options
+      #TODO: add check between type and default value, in the main class,
+      # Thor already does it.
+      tophat.options={:parameter_xxx=>{:type=>:numeric, :default=>10}}
+      tophat.params={:fake_parameter=>01}
+      tophat.normalize_params.should == "--parameter_xxx=10"
+    end
+  end
+end
+
+
+# describe Tophat do
+#   describe "Tophat" do
+#     it "the program is " do
+#       Bio::Ngs::Tophat.new.program.should == Bio::Ngs::Utils.binary("tophat/tophat")
+#     end
+#     
+#     it "returns the default parameters" do
+#       Bio::Ngs::Tophat.new.main.should == ""
+#     end
+#     
+#     it "all the parameters of this application" do 
+#       first_option = Bio::Ngs::Tophat.tasks["main"].options.first #is an array of name, Thor::Option
+#       thor_option = first_option.last
+#       thor_option.name.should == "reads"
+#     end
+#     
+#   end
+# end

data/spec/utils_spec.rb

@@ -0,0 +1,22 @@
+#
+#  converter_qseq_spec.rb - RSpec Test
+#
+# Copyright:: Copyright (C) 2011
+#     Raoul Bonnal <r@bioruby.org>
+# License:: The Ruby License
+#
+#
+
+
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Utils" do
+  it "tags the regular file name with the new tag and extension" do
+    Bio::Ngs::Utils.tag_filename("test_file_name.txt", "report", "csv").should == "test_file_name_report.csv"    
+  end
+  
+  it "tags the strange file name with the new tag and extension" do
+    Bio::Ngs::Utils.tag_filename("test_file_name", "report", "csv").should == "test_file_name_report.csv"    
+  end
+  
+end

data/test/conf/test_db.yml

@@ -0,0 +1,4 @@
+adapter: sqlite3
+database: test/data/test.sqlite3
+pool: 5
+timeout: 5000

data/test/data/blastoutput.xml

@@ -0,0 +1,69 @@
+<?xml version="1.0"?>
+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
+<BlastOutput>
+  <BlastOutput_program>blastx</BlastOutput_program>
+  <BlastOutput_version>blastx 2.2.19 [Nov-02-2008]</BlastOutput_version>
+  <BlastOutput_reference>~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~&quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs&quot;,  Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
+  <BlastOutput_db>uniprot_sprot</BlastOutput_db>
+  <BlastOutput_query-ID>lcl|1_0</BlastOutput_query-ID>
+  <BlastOutput_query-def>ENSBTAG00000025113_499_35</BlastOutput_query-def>
+  <BlastOutput_query-len>1221</BlastOutput_query-len>
+  <BlastOutput_param>
+    <Parameters>
+      <Parameters_matrix>BLOSUM62</Parameters_matrix>
+      <Parameters_expect>10</Parameters_expect>
+      <Parameters_gap-open>11</Parameters_gap-open>
+      <Parameters_gap-extend>1</Parameters_gap-extend>
+      <Parameters_filter>F</Parameters_filter>
+    </Parameters>
+  </BlastOutput_param>
+  <BlastOutput_iterations>
+    <Iteration>
+      <Iteration_iter-num>239</Iteration_iter-num>
+      <Iteration_query-ID>lcl|239_0</Iteration_query-ID>
+      <Iteration_query-def>ENSBTAG00000031386_1906_35</Iteration_query-def>
+      <Iteration_query-len>2107</Iteration_query-len>
+      <Iteration_hits>
+        <Hit>
+          <Hit_num>1</Hit_num>
+          <Hit_id>sp|Q5TTP0|WDY_ANOGA</Hit_id>
+          <Hit_def>WD repeat-containing protein on Y chromosome OS=Anopheles gambiae GN=WDY PE=4 SV=4</Hit_def>
+          <Hit_accession>Q5TTP0</Hit_accession>
+          <Hit_len>1059</Hit_len>
+          <Hit_hsps>
+            <Hsp>
+              <Hsp_num>1</Hsp_num>
+              <Hsp_bit-score>224.172</Hsp_bit-score>
+              <Hsp_score>570</Hsp_score>
+              <Hsp_evalue>2.55108e-57</Hsp_evalue>
+              <Hsp_query-from>1</Hsp_query-from>
+              <Hsp_query-to>1641</Hsp_query-to>
+              <Hsp_hit-from>347</Hsp_hit-from>
+              <Hsp_hit-to>897</Hsp_hit-to>
+              <Hsp_query-frame>1</Hsp_query-frame>
+              <Hsp_identity>167</Hsp_identity>
+              <Hsp_positive>271</Hsp_positive>
+              <Hsp_gaps>19</Hsp_gaps>
+              <Hsp_align-len>566</Hsp_align-len>
+              <Hsp_qseq>KGILCFDYCPDRNVLVTGGYDPLIRLWNPFFSRKPVWMMKGHQTSVTHIVVNSKDSSILLSVSKDKNIRVWDMQDYQCLQSFCGFSEV-IKGTWICALGLKWGHGFGIGILKGYLETQGPGRAEEKTT--TYSTPLCAVLYSKVFKQVVSGCLSGMVSVWEVVTGRRLMEFSVTGDQ-------QVELTAMSLDESEGCLLTGLRDGTVKMWNYSVGECLLTFPKADQLEISGIVHMNKVFYTTGWSKRIT-YYTFHKIKPVLLCHHWQTFHTEDVLSMAKYQNQ--FIATSSYNGDILFWNVGTFRPTQRALASDPQPRRPLSPVRGLRDQLKGKKQTSRRSCCCSPMHR--WRRLAMFSQPSGC-HIEVLTFFLIIFLQTRPRLPHSAALLSSCMDGYIYAWSIHGSGGLLGKFPXXXXXXXXXXXXAMATDQNDWILVTGDCKGCIKIWDIKD-YCAHSDK-QTNHPSEINKFRFLISERIQVSLPNYSPPEEKKVEAGQTISLIPPQLLISWKAHLDSVADILYVDSLQLVISAGQDRDVKAWKLSGDAIGTFGLSV-WKRL</Hsp_qseq>
+              <Hsp_hseq>RGVTCFAFEPSNELLVSGGPDCDLRLWDIHRPEKPSVVLVGHTSSITFLFLQDAGEKIY-SLDQRKIIKVWDVRNRVLLQTFGQFSTVLVKGVPACAYYNKRARELVVASNKLFVTACCPEIALDRTDGESHTKPVSVLLYNGLYRLVVSCGFDSFIIVWDHRVNRKMTIITEAHTQIRNGVLEPVEITAACFDGKEQMLLTGARNGSLKIWNIGGRTCMRTIQIEEDCEVTGVFWQANRILAMGWNHRVVEFAAFAEQDEYPRGLQWRKQHSDDILCAAVSGSEPGVMATCSYAGELVFWMLETGQPYRRYDATNPRTRLPISFREGRADLMKPRKLTPRRSLFQMPPGQLAHRRLTRILMPSGLEQMRQLSIQALLFLAMRKMLPDRGTLFGSLDNGMVQVWSHHPDGGFKGQF--NGIHMAGDRIITLATDKANRFLFTGTALGYVKTWYIENCWIPNEDKFHVNKPALRILFPFLLNDVV--------PGRAKRSARAQ----VKPWLLNSYQAHRACVTGLTYLDDTGLLLSCSSDRTVRLWTLGGRYIGLLGSPVNWQPL</Hsp_hseq>
+              <Hsp_midline>+G+ CF + P   +LV+GG D  +RLW+     KP  ++ GH +S+T + +      I  S+ + K I+VWD+++   LQ+F  FS V +KG   CA   K      +   K ++    P  A ++T   +++ P+  +LY+ +++ VVS      + VW+    R++   +    Q        VE+TA   D  E  LLTG R+G++K+WN     C+ T    +  E++G+          GW+ R+  +  F +         W+  H++D+L  A   ++   +AT SY G+++FW + T +P +R  A++P+ R P+S   G  D +K +K T RRS    P  +   RRL     PSG   +  L+   ++FL  R  LP    L  S  +G +  WS H  GG  G+F              +ATD+ +  L TG   G +K W I++ +  + DK   N P+    F FL+++ +        P   K+    Q    + P LL S++AH   V  + Y+D   L++S   DR V+ W L G  IG  G  V W+ L</Hsp_midline>
+            </Hsp>
+          </Hit_hsps>
+        </Hit>
+      </Iteration_hits>
+      <Iteration_stat>
+        <Statistics>
+          <Statistics_db-num>525997</Statistics_db-num>
+          <Statistics_db-len>185874894</Statistics_db-len>
+          <Statistics_hsp-len>0</Statistics_hsp-len>
+          <Statistics_eff-space>0</Statistics_eff-space>
+          <Statistics_kappa>0.041</Statistics_kappa>
+          <Statistics_lambda>0.267</Statistics_lambda>
+          <Statistics_entropy>0.14</Statistics_entropy>
+        </Statistics>
+      </Iteration_stat>
+    </Iteration>
+ </BlastOutput_iterations>
+</BlastOutput>
+