Moved used datasets to /isnt/extdata (#25)

inst/extdata/BAPS_format_clustering_diploid.txt

@@ -0,0 +1,10 @@
+-9 102 56 80 100 90 118 90 88 104 1
+-9 102 54 82 102 92 116 90 86 104 1
+88 104 56 84 102 -9 120 90 88 100 2
+86 102 56 80 102 -9 116 90 86 100 2
+88 102 54 80 102 90 116 92 -9 100 3
+88 102 56 80 100 90 118 90 -9 104 3
+80 102 54 82 102 92 116 90 86 104 4
+88 104 56 84 102 92 120 90 88 100 4
+86 102 56 80 -9 90 116 90 86 100 5
+88 102 54 80 -9 90 116 92 86 100 5

inst/extdata/FASTA_clustering_haploid.fasta

@@ -0,0 +1,20 @@
+>1
+AACGAAACGATCGCGTCACCGGAACGTTGTCCGTCTCGAATAGCACTGTGGGAACGTGTTTTACATTCGT
+TAGTAACATGGTCAGCTGCTCATCCGTATT
+
+>2
+ATCAGCAAACGAGAAGTTGCAGAGGTCTTTGGTTTGAGCATTGCCCCCATACAATCGACTTCTGGCCTGG
+AATGCACCACAAACATACCCCACAGGCTCG
+
+>3
+GCTTTTACTAAGGCCTATCGGATTCAACGTCACTAAGACTCGGCACTAACAGGCCGTTGTAAGCCGCTCT
+GTCTGAGTATGGATGGTGGAGGCGGAGCCG
+
+>4
+ACCTGGACCTCTGTATTAACGGCTGTGATTCTGAGGGGGGTATCGCAGCGCACTTTCTAGCTATATCACG
+CAAGGATAAAGTTCACCCATCACGTTGACC
+
+>5
+ACAATACGTCATCCACACCGCGCCTATGGAAGAATTTGCCCTTTCGGCGACAGCCCATGCTGTCAAGGAG
+GTAACATAGCTACCAGGTCCCATTCCAGGA
+

inst/extdata/sam_example.sam

@@ -0,0 +1,12 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:1	LN:249250621	AS:NCBI37	UR:file:/data/local/ref/GATK/human_g1k_v37.fasta	M5:1b22b98cdeb4a9304cb5d48026a85128
+@SQ	SN:2	LN:243199373	AS:NCBI37	UR:file:/data/local/ref/GATK/human_g1k_v37.fasta	M5:a0d9851da00400dec1098a9255ac712e
+@SQ	SN:3	LN:198022430	AS:NCBI37	UR:file:/data/local/ref/GATK/human_g1k_v37.fasta	M5:fdfd811849cc2fadebc929bb925902e5
+@RG	ID:UM0098:1	PL:ILLUMINA	PU:HWUSI-EAS1707-615LHAAXX-L001	LB:80	DT:2010-05-05T20:00:00-0400	SM:SD37743	CN:UMCORE
+@RG	ID:UM0098:2	PL:ILLUMINA	PU:HWUSI-EAS1707-615LHAAXX-L002	LB:80	DT:2010-05-05T20:00:00-0400	SM:SD37743	CN:UMCORE
+@PG	ID:bwa	VN:0.5.4
+@PG	ID:GATK TableRecalibration	VN:1.0.3471	CL:Covariates=[ReadGroupCovariate, QualityScoreCovariate, CycleCovariate, DinucCovariate, TileCovariate], default_read_group=null, default_platform=null, force_read_group=null, force_platform=null, solid_recal_mode=SET_Q_ZERO, window_size_nqs=5, homopolymer_nback=7, exception_if_no_tile=false, ignore_nocall_colorspace=false, pQ=5, maxQ=40, smoothing=1
+1:497:R:-272+13M17D24M	113	1	497	37	37M	15	100338662	0	CGGGTCTGACCTGAGGAGAACTGTGCTCCGCCTTCAG	0;==-==9;>>>>>=>>>>>>>>>>>=>>>>>>>>>>	XT:A:U	NM:i:0	SM:i:37	AM:i:0	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:37
+19:20389:F:275+18M2D19M	99	1	17644	0	37M	=	17919	314	TATGACTGCTAATAATACCTACACATGTTAGAACCAT	>>>>>>>>>>>>>>>>>>>><<>>><<>>4::>>:<9	RG:Z:UM0098:1	XT:A:R	NM:i:0	SM:i:0	AM:i:0	X0:i:4	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:37
+19:20389:F:275+18M2D19M	147	1	17919	0	18M2D19M	=	17644	-314	GTAGTACCAACTGTAAGTCCTTATCTTCATACTTTGT	;44999;499<8<8<<<8<<><<<<><7<;<<<>><<	XT:A:R	NM:i:2	SM:i:0	AM:i:0	X0:i:4	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:18^CA19
+9:21597+10M2I25M:R:-209	83	1	21678	0	8M2I27M	=	21469	-244	CACCACATCACATATACCAAGCCTGGCTGTGTCTTCT	<;9<<5><<<<><<<>><<><>><9>><>>>9>>><>	XT:A:R	NM:i:2	SM:i:0	AM:i:0	X0:i:5	X1:i:0	XM:i:0	XO:i:1	XG:i:2	MD:Z:35

inst/extdata/vcf_example.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Genotype Probabilities">
+##FORMAT=<ID=PL,Number=G,Type=Float,Description="Phred-scaled Genotype Likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMP001	SAMP002
+20	1291018	rs11449	G	A	.	PASS	.	GT	0/0	0/1
+20	2300608	rs84825	C	T	.	PASS	.	GT:GP	0/1:.	0/1:0.03,0.97,0
+20	2301308	rs84823	T	G	.	PASS	.	GT:PL	./.:.	1/1:10,5,0