added tests back

tests/data/b16.f10/b16.expressed.vcf

@@ -0,0 +1,4 @@
+##reference=mm10
+#chr	pos	id	ref	alt	qual	filter	info
+chr9	82927102	.	G	T	.	.	.
+chrX	8125624	.	C	A	.	.	.

tests/data/b16.f10/b16.f10.127a.aldh1b1.chr4.45802539.refG.altC.sam

@@ -0,0 +1,39 @@
+@HD VN:1.0  SO:coordinate
+@SQ SN:chr1 LN:195471971
+@SQ SN:chr2 LN:182113224
+@SQ SN:chr3 LN:160039680
+@SQ SN:chr4 LN:156508116
+@SQ SN:chr5 LN:151834684
+@SQ SN:chr6 LN:149736546
+@SQ SN:chr7 LN:145441459
+@SQ SN:chr8 LN:129401213
+@SQ SN:chr9 LN:124595110
+@SQ SN:chr10    LN:130694993
+@SQ SN:chr11    LN:122082543
+@SQ SN:chr12    LN:120129022
+@SQ SN:chr13    LN:120421639
+@SQ SN:chr14    LN:124902244
+@SQ SN:chr15    LN:104043685
+@SQ SN:chr16    LN:98207768
+@SQ SN:chr17    LN:94987271
+@SQ SN:chr18    LN:90702639
+@SQ SN:chr19    LN:61431566
+@SQ SN:chrX LN:171031299
+@SQ SN:chrY LN:91744698
+@SQ SN:chrM LN:16299
+@RG ID:Tumor_B16_F10_0810_127A  PL:ILLUMINA PU:HiSeq2500    LB:Tumor_B16_F10_0810_127A  DS:rnaseq   SM:Tumor_B16_F10_0810_127A  CN:MSSM
+HWI-D00273:119:C7FUMANXX:2:2314:9979:73514	163	chr4	45693473	255	13M145161N88M	=	45838774	145402	GTGCCAAAGAGACCGACACTCTTGGTGCTCGGGGTACAGTCTCCTCAAAAGTTCCCCTCTTCTGTTTTATAAGATAGGCTTTGAGGGTGCGATGCGCACGC	CCCCCGGGGG1@FBGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGFGGGGGGGGGGGGGGGGGG	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:1	AS:i:196	XS:A:-
+HWI-D00273:119:C7FUMANXX:2:1302:1900:88137	147	chr4	45799162	255	8M3285N93M	=	45799073	-3475	CACCGCAGGTCCTCAGGATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCG	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGFEGGGGGGFC@DB<GAACBB	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:203	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:1304:19043:33867	163	chr4	45799164	255	6M3285N95M	=	45802895	3832	CCGCAGGTCCTCAGGATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAA	ABA=AE<CDGGGGGB@GGGGGFGGGGGEGDCGBGGGGGGGGGGDG>/EFGGEGGGGGE1@@FGGG<FGFGGBGD00C09FFCEC>FGGGBC00FDFG@.FG	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:201	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:1309:15476:29614	83	chr4	45799165	255	5M3285N96M	=	45799092	-3459	CGCAGGTCCTCAGGATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAAC	GGGGGC<GGG@@CGEGGGGGGGFGGGGECGBGB>GGGGGGGGEBGGGGEGGGGGG>GGGF@DGGGGGGGGEGFC1FGGF>GGF11EE1DFBGE=/;A<3A3	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:1	AS:i:201	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:2109:16809:15061	83	chr4	45799165	255	5M3285N96M	=	45799092	-3459	CGCAGGTCCTCAGGATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAAC	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGGF=GGGECCCBC	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:203	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:2115:6797:61925	163	chr4	45802455	255	101M	=	45802642	288	GTCCTCAGGATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAAT	BBC=BGCGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGFGGGGGGGGGGGFDEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDAGGGGEB	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:200
+HWI-D00273:119:C7FUMANXX:2:1106:19607:76744	83	chr4	45802460	255	101M	=	45799110	-3451	CAGGATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAA	GGGGGFGGGGGGGGGGGGFGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGCCCCC	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:201	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:2109:18038:25161	83	chr4	45802466	255	101M	=	45799093	-3474	GCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAG	EGGGGG:GGGDGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGFGGE>GGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGCCCCC	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:201	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:2310:14056:99606	147	chr4	45802468	255	101M	=	45799077	-3492	TGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAG	GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGFGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:201	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:2314:15707:68909	83	chr4	45802468	255	101M	=	45799080	-3489	TGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAG	CGGDGGGGGGGGEEFDGGADGGGEBGGGGGGE8>GGGGFCG@CGFDEGGF:DGFF>GGGGEGDGEGGGGGGGGFDGGGGGDGGEGDDE>BGGGFFGB@@BB	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:3	AS:i:195	XS:A:+
+HWI-D00273:119:C7FUMANXX:2:1110:20436:75562	99	chr4	45802487	255	101M	=	45802556	170	GCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAGATTTGCTACAACAAGCTGT	CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGG	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:200
+HWI-D00273:119:C7FUMANXX:2:1206:18456:69465	99	chr4	45802491	255	101M	=	45802525	135	CGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAGATTTGCTACAACAAGCTGTTCAT	CBCCCCFGEGGGGGGGGGGGGGGFGGGGGGGGFGGGGGGGGGGGGGGGEEDGGGGEGGGGGGGGGGGGGFGGGGGGGBCGFGGGGGGGGGGGGG>FFGGGG	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:200
+HWI-D00273:119:C7FUMANXX:2:2310:16660:100528	163	chr4	45802498	255	101M	=	45802719	322	TCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAGATTTGCTACAACAAGCTGTTCATCAACAAC	BCCBCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGBB	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:200
+HWI-D00273:119:C7FUMANXX:2:1206:18456:69465	147	chr4	45802525	255	101M	=	45802491	-135	ACTCTACAGCAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAGATTTGCTACAACAAGCTGTTCATCAACAACGAGTGGCATGATGCGGTCAGCAAAAAG	8GGGE>>@GGGGGCFC8E=GGGGGCGBGD@@GGGGGDGGGGGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDCGDGGGGGGGGGGGBBBAB	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:200
+HWI-D00273:119:C7FUMANXX:2:1216:11959:66492	83	chr4	45802534	255	101M	=	45799111	-3524	CAGCTGCTCTCCCGAACCCAATCCCAAACCCAGAGATTTGCTACAACAAGCTGTTCATCAACAACGAGTGGCATGATGCGGTCAGCAAAAAGACCTTCCCC	GDGGGGGGGGGGGGF=GGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGFGGFGGGGGGGGGGFFGGGGGGGGGGGGGGGEGGGGGGGGGGGGGGGGBCCCC	RG:Z:Tumor_B16_F10_0810_127A	NH:i:1	HI:i:1	nM:i:0	AS:i:201	XS:A:+