Fixes to fastaFromBed maskFastaFromBed

	1. Fixed bugs in parsing command line booleans in fastaFromBed and maskFastaFromBed
	2. Added tabular output to fastaFromBed

data/grauberCNVs.mm9.bed

+chr1	80693538	80756245	3
+chr1	113155258	113353811	8
+chr1	165623847	165687473	10
+chr1	83527681	83670336	4
+chr1	109799574	109846577	7
+chr1	139561033	139755800	9
+chr1	171540729	171602435	11
+chr1	29622679	29679823	1
+chr1	41323064	41384953	2
+chr1	88098429	88192488	5
+chr1	101057225	101116461	6
+chr2	46300322	46429107	12
+chr2	113903268	114046208	13
+chr2	149617829	149685000	14
+chr2	150769441	150977588	15
+chr2	153616888	153650723	16
+chr3	15143136	15227170	69
+chr3	105597837	105786967	20
+chr3	23407418	23461110	17
+chr3	24641609	24677698	18
+chr3	91643519	91735051	19
+chr4	77062265	77097263	21
+chr4	142262278	142306672	23
+chr5	92099175	93717000	73
+chr5	5976057	6102460	24
+chr5	10889821	11342371	71
+chr5	14280030	14533608	72
+chr5	19128651	19301711	25
+chr5	45115739	45245946	26
+chr6	130893363	131110204	31
+chr6	41217003	41326245	27
+chr6	59919199	60574840	28
+chr6	68849161	68972398	29
+chr6	130689944	130887826	30
+chr7	14502598	14907637	75
+chr7	18214789	20091007	76
+chr7	27939361	29941523	77
+chr7	10756862	11256183	74
+chr7	105633007	105755099	34
+chr7	107159323	107731942	35
+chr7	126994428	127015786	36
+chr8	54070261	54703878	78
+chr9	38513513	38890920	38
+chr10	22130708	22442271	40
+chr10	22026436	22125980	39
+chr11	70889232	71011866	41
+chr11	73872418	73983087	42
+chr12	63410403	64003912	45
+chr12	109902238	110029377	46
+chr12	10884637	10926537	43
+chr12	38675139	38736567	44
+chr13	62832969	63562683	79
+chr13	27454053	27561881	47
+chr13	60124305	60237782	48
+chr13	96207986	96272747	49
+chr14	41248736	42250486	80
+chr14	26238871	26374471	50
+chr14	39102695	39249776	51
+chr14	65456690	65666567	52
+chr14	100952862	101002308	53
+chr14	110369978	110416948	54
+chr15	14877412	14997101	55
+chr15	100394029	100429768	56
+chr16	11955278	12139976	57
+chr16	34340957	34419780	58
+chr16	35173865	35211657	59
+chr17	20875084	21013298	60
+chr17	25414459	25648357	61
+chr17	28671435	29145123	62
+chr17	36737135	36967135	63
+chr18	57910954	57993795	64
+chr19	8395584	8572455	65
+chr19	10618260	10706499	66
+chr19	25173870	25201397	67

data/hallPublishedCNVs.mm9.bed

+chr1	28189175	28227575	CNV-1	1
+chr1	90108087	90169544	CNV-34	1
+chr1	123583095	123596701	CNV-2	1
+chr1	124850985	124851051	INTRA-5	15
+chr2	18208702	18225394	CNV-19	1
+chr2	94313866	94333722	CNV-11	1
+chr2	134972469	134997832	CNV-18	1
+chr3	105929453	106113283	CNV-26	1
+chr3	23256014	23256081	INTRA-5	9
+chr3	75901339	75901394	INTRA-5	18
+chr3	75936734	75936764	INTRA-5	6
+chr3	103693274	103713534	CNV-9	1
+chr3	115298132	115298172	INTRA-5	21
+chr5	57785801	57785852	INTRA-5	22
+chr6	18861763	19717247	INTRA-7	1
+chr6	60629050	60987404	CNV-15	1
+chr6	8007236	8007264	INTRA-5	24
+chr6	47067586	47120806	CNV-35	1
+chr6	100178586	100183256	CNV-31A	1
+chr7	3668236	3865944	CNV-33	1
+chr7	21479670	21479936	CNV-38	1
+chr7	22773017	22773063	CNV-38	2
+chr7	22956667	22956699	CNV-38	4
+chr7	23814776	23814801	CNV-38	3
+chr7	27093609	27112171	CNV-25	1
+chr7	48550958	48551012	INTRA-5	20
+chr7	132458696	132477475	CNV-13	1
+chrX	144235798	146533819	CNV-24	1
+chrX	7965346	7965679	INTRA-5	14
+chrX	69822118	69822220	INTRA-5	8
+chrX	117321114	117321161	INTRA-5	25
+chrX	166407713	166446984	CNV-32	1
+chr10	89343808	89412251	CNV-16	1
+chr10	10231025	10231079	INTRA-5	12
+chr11	99060096	99107670	INTRA-2	1
+chr12	56180013	56406524	CNV-37	1
+chr12	42023915	42032768	CNV-7	1
+chr12	61107103	61107161	INTRA-5	19
+chr12	83103241	83164905	CNV-36	1
+chr13	27972538	27972616	INTRA-5	5
+chr13	66187169	66187832	CNV-31B	1
+chr13	66328547	66328631	CNV-31B	2
+chr13	66730000	66780000	CNV-31B	3
+chr13	72011795	72015700	CNV-12	1
+chr13	79438629	79455024	CNV-6	1
+chr13	80180000	80180059	INTRA-5	3
+chr14	81745411	97145513	INTRA-5	1
+chr14	88055623	88089049	INTRA-3	1
+chr14	23721913	23752071	CNV-5	1
+chr14	26694338	27113047	CNV-29	1
+chr14	69872184	70090645	CNV-20	1
+chr14	83603387	83695459	INTRA-5	10
+chr14	52779156	52808797	CNV-17	1
+chr14	53457755	53457787	CNV-21	1
+chr14	53471679	53474905	CNV-21	2
+chr14	86899205	86899322	INTRA-5	16
+chr14	86921675	86921743	INTRA-5	17
+chr14	88047739	88048445	INTRA-5	2
+chr14	88179301	88179408	INTRA-5	23
+chr14	88500104	88500196	INTRA-5	26
+chr14	91810581	91820000	INTRA-5	27
+chr14	91820000	91830000	INTRA-5	28
+chr14	91830000	91835696	INTRA-5	29
+chr14	121441084	121441140	INTRA-5	13
+chr15	67746820	67746888	INTRA-5	7
+chr16	24620313	24643779	CNV-4	1
+chr16	45980543	46009273	CNV-10	1
+chr16	6115740	6138128	CNV-8	1
+chr16	86916835	86916862	INTRA-5	11
+chr17	27424989	27585750	CNV-22	1
+chr17	30663019	31096355	INTRA-1	1
+chr17	6904628	6904691	CNV-30	1
+chr17	15098411	15190749	CNV-27	1
+chr17	83083382	83083495	INTRA-5	4
+chr18	28487329	28506543	CNV-14	1
+chr18	86713560	86722649	CNV-3	1
+chr19	37336315	37433017	INTRA-8	1
+chrX_random	462207	462270	CNV-24	2

src/bamToBed/bamToBed.cpp

@@ -229,4 +229,4 @@ bool IsCorrectMappingForBEDPE (const BamAlignment &bam) {
 		return true;
 	}
 	else return false;
-}
\ No newline at end of file
+}

src/fastaFromBed/a.bed

+chr1	5	10	me	1	+

src/fastaFromBed/fasta

+>chr1
+acagagagacskdjhfsdlfkngsl'dkfbmnsldfkbnslfkgm
+