Updated test case for mm10 in pileup mode and rebased.

Author: PolinaBevad

testdata/integrationtestcases/Simple;mm10.fa;T7-75_S10_chr10_DEL.bam;chr10;11291400-11295300;-f 0.001;.txt

@@ -3944,6 +3944,7 @@ T7-75_S10_chr10_DEL	testbed	10	11295243	11295243	T	T	1203	0	632	571	0	0	T/T	0	2;
 T7-75_S10_chr10_DEL	testbed	10	11295236	11295236	C	T	1165	1	621	543	1	0	C/T	0.0009	2;0	60.0	0	12.0	0	255.0	0	0	0	4	1.000	1	7.0	0	1146	GGTATGGCGATTCAGTACTG	ATTTTGTTCTGTTAATGACT	10:11291401-11295300	SNV	0	0
 T7-75_S10_chr10_DEL	testbed	10	11295237	11295237	A	G	1164	3	620	540	2	1	A/G	0.0026	2;2	27.0	1	17.3	1	255.0	0.500	0.0009	0.0009	3	4.000	1	1.3	1	1133	GTATGGCGATTCAGTACTGC	TTTTGTTCTGTTAATGACTG	10:11291401-11295300	SNV	0	0
 T7-75_S10_chr10_DEL	testbed	10	11295237	11295237	A	T	1164	1	620	540	1	0	A/T	0.0009	2;0	64.0	0	12.0	0	255.0	0	0	0	3	4.000	1	3.0	0	1133	GTATGGCGATTCAGTACTGC	TTTTGTTCTGTTAATGACTG	10:11291401-11295300	SNV	0	0
+T7-75_S10_chr10_DEL	testbed	10	11295238	11295238	T	T	1164	0	623	540	0	0	T/T	0	2;0	39.5	1	39.8	1	254.8	57.150	0.9991	0	0	0	0	0.4	1143	1144	0	0	10:11291401-11295300		0	0
 T7-75_S10_chr10_DEL	testbed	10	11295237	11295238	AT	A	1164	1	623	540	1	0	T/-1	0.0009	2;0	42.0	0	41.0	0	255.0	2.000	0.0009	0	3	4.000	1	0	1	1144	GTATGGCGATTCAGTACTGC	TTTGTTCTGTTAATGACTGG	10:11291401-11295300	Deletion	0	0
 T7-75_S10_chr10_DEL	testbed	10	11295239	11295239	T	T	1165	0	624	541	0	0	T/T	0	2;0	39.6	1	39.8	1	254.8	54.476	1.0000	0	0	0	0	0.4	1144	1144	0	0	10:11291401-11295300		0	0
 T7-75_S10_chr10_DEL	testbed	10	11295232	11295232	A	C	1093	1	614	477	1	0	A/C	0.0009	2;0	21.0	0	12.0	0	255.0	0	0	0	0	1.000	1	2.0	0	1064	TCTAGGTATGGCGATTCAGT	CTGCATTTTGTTCTGTTAAT	10:11291401-11295300	SNV	0	0