diff --git a/public/testdata/inttestbgl.gprobs b/public/testdata/Beagle/inttestbgl.gprobs
similarity index 100%
rename from public/testdata/inttestbgl.gprobs
rename to public/testdata/Beagle/inttestbgl.gprobs
diff --git a/public/testdata/inttestbgl.input.vcf b/public/testdata/Beagle/inttestbgl.input.vcf
similarity index 100%
rename from public/testdata/inttestbgl.input.vcf
rename to public/testdata/Beagle/inttestbgl.input.vcf
diff --git a/public/testdata/inttestbgl.like b/public/testdata/Beagle/inttestbgl.like
similarity index 100%
rename from public/testdata/inttestbgl.like
rename to public/testdata/Beagle/inttestbgl.like
diff --git a/public/testdata/inttestbgl.output.vcf b/public/testdata/Beagle/inttestbgl.output.vcf
similarity index 100%
rename from public/testdata/inttestbgl.output.vcf
rename to public/testdata/Beagle/inttestbgl.output.vcf
diff --git a/public/testdata/inttestbgl.phased b/public/testdata/Beagle/inttestbgl.phased
similarity index 100%
rename from public/testdata/inttestbgl.phased
rename to public/testdata/Beagle/inttestbgl.phased
diff --git a/public/testdata/inttestbgl.r2 b/public/testdata/Beagle/inttestbgl.r2
similarity index 100%
rename from public/testdata/inttestbgl.r2
rename to public/testdata/Beagle/inttestbgl.r2
diff --git a/public/testdata/PhaseByTransmission.IntegrationTest.FP.vcf b/public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.FP.vcf
similarity index 100%
rename from public/testdata/PhaseByTransmission.IntegrationTest.FP.vcf
rename to public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.FP.vcf
diff --git a/public/testdata/PhaseByTransmission.IntegrationTest.Special.vcf b/public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.Special.vcf
similarity index 100%
rename from public/testdata/PhaseByTransmission.IntegrationTest.Special.vcf
rename to public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.Special.vcf
diff --git a/public/testdata/PhaseByTransmission.IntegrationTest.TN.vcf b/public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TN.vcf
similarity index 100%
rename from public/testdata/PhaseByTransmission.IntegrationTest.TN.vcf
rename to public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TN.vcf
diff --git a/public/testdata/PhaseByTransmission.IntegrationTest.TP.vcf b/public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf
similarity index 100%
rename from public/testdata/PhaseByTransmission.IntegrationTest.TP.vcf
rename to public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.TP.vcf
diff --git a/public/testdata/PhaseByTransmission.IntegrationTest.goodFamilies.ped b/public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped
similarity index 100%
rename from public/testdata/PhaseByTransmission.IntegrationTest.goodFamilies.ped
rename to public/testdata/PhaseByTransmission/PhaseByTransmission.IntegrationTest.goodFamilies.ped
diff --git a/public/testdata/ROD_validation/always_reindex.vcf b/public/testdata/ROD_validation/always_reindex.vcf
deleted file mode 100755
index 2a3dcb483..000000000
--- a/public/testdata/ROD_validation/always_reindex.vcf
+++ /dev/null
@@ -1,7 +0,0 @@
-##fileformat=VCFv4.0
-##fileDate=20090908
-##source=QCALLv1.0
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
-1	17786644	rs34417109	G	A	60.0	PASS	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	
diff --git a/public/testdata/ROD_validation/newerTribbleTrack.vcf b/public/testdata/ROD_validation/newerTribbleTrack.vcf
deleted file mode 100755
index 2a3dcb483..000000000
--- a/public/testdata/ROD_validation/newerTribbleTrack.vcf
+++ /dev/null
@@ -1,7 +0,0 @@
-##fileformat=VCFv4.0
-##fileDate=20090908
-##source=QCALLv1.0
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
-1	17786644	rs34417109	G	A	60.0	PASS	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	
diff --git a/public/testdata/ROD_validation/read_only/good_index.vcf b/public/testdata/ROD_validation/read_only/good_index.vcf
deleted file mode 100755
index 41588ab52..000000000
--- a/public/testdata/ROD_validation/read_only/good_index.vcf
+++ /dev/null
@@ -1,7 +0,0 @@
-##format=VCRv3.2
-##fileDate=20090908
-##source=QCALLv1.0
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
-1	17786644	rs34417109	G	A	60.0	0	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	
diff --git a/public/testdata/ROD_validation/read_only/no_index.vcf b/public/testdata/ROD_validation/read_only/no_index.vcf
deleted file mode 100755
index 41588ab52..000000000
--- a/public/testdata/ROD_validation/read_only/no_index.vcf
+++ /dev/null
@@ -1,7 +0,0 @@
-##format=VCRv3.2
-##fileDate=20090908
-##source=QCALLv1.0
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA06985	NA06986	NA06994	NA07000	NA07037	NA07051	NA07346	NA07347	NA07357	NA10847	NA10851	NA11829	NA11830	NA11831	NA11832	NA11840	NA11881	NA11894	NA11918	NA11919	NA11920	NA11931	NA11992	NA11993	NA11994	NA11995	NA12003	NA12004	NA12005	NA12006	NA12043	NA12044	NA12045	NA12144	NA12154	NA12155	NA12156	NA12234	NA12249	NA12287	NA12414	NA12489	NA12716	NA12717	NA12749	NA12750	NA12751	NA12760	NA12761	NA12762	NA12763	NA12776	NA12812	NA12813	NA12814	NA12815	NA12828	NA12872	NA12873	NA12874	NA12878	NA12891	NA12892
-1	17786644	rs34417109	G	A	60.0	0	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	
diff --git a/public/testdata/ROD_validation/read_only/relic.vcf b/public/testdata/ROD_validation/read_only/relic.vcf
deleted file mode 100755
index 41588ab52..000000000
--- a/public/testdata/ROD_validation/read_only/relic.vcf
+++ /dev/null
@@ -1,7 +0,0 @@
-##format=VCRv3.2
-##fileDate=20090908
-##source=QCALLv1.0
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-##phasing=partial
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-1	17786644	rs34417109	G	A	60.0	0	NS=60;DP=279;AN=126;AC=6;AA=G;DB=1	GT:GQ:DP:HQ	0|0:90:1:93,93	0|0:84:13:88,85	0|0:90:3:93,93	0|0:90:11:93,93	0|0:9:4:9,93	0|0:90:5:93,93	0|0:90:2:93,93	1|0:44:2:44,88	0|0:90:7:93,93	0/0:52:3	1/0:49:13	0|0:90:3:93,93	0|0:87:2:93,87	0|0:4:0:4,57	0|0:26:2:26,73	0|0:90:7:93,93	0|0:90:4:93,93	0|0:90:2:93,93	0|0:57:1:93,57	0|0:46:3:93,46	0|0:90:18:93,93	0|0:90:5:93,93	0|1:48:9:65,48	0|0:90:2:93,93	0|0:90:3:93,93	0|0:90:5:93,93	0|0:43:8:93,43	0/0:60:2	0|0:90:9:93,93	0|0:37:6:37,93	0|0:90:1:93,93	0|0:90:3:93,93	0|0:90:4:93,93	0|0:46:4:93,46	0|0:90:3:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|0:90:1:93,93	0|0:87:6:88,93	0|0:83:3:83,93	0/0:37:6	0|0:90:6:93,93	0|0:90:5:93,93	0/0:93:1	0|0:90:16:93,93	0|0:90:3:93,93	0|0:57:8:57,93	0|1:49:3:65,49	0|0:90:4:93,93	0|0:90:2:93,93	0|0:90:5:93,93	0|1:42:2:46,44	0|0:90:4:93,93	0|0:90:2:93,93	0|0:26:5:93,26	0|0:90:2:93,93	1|0:4:4:4,93	0|0:90:7:93,93	0|0:90:2:93,93	0|0:66:2:66,93	0/0:60:0	0|0:4:0:57,4	0|0:90:3:93,93	
diff --git a/public/testdata/complexExample.vcf4 b/public/testdata/complexExample.vcf4
new file mode 100644
index 000000000..0aa1f6d71
--- /dev/null
+++ b/public/testdata/complexExample.vcf4
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##source=ArbitrarySource
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
+##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##reference=human_b36_both.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+1	10001292	testid1	G	A	12.22	PASS	AF=0.50;AlleleBalance=0.57;DoC=23;HomopolymerRun=0;MAPQ0=8;NS=1;RMSMAPQ=46.31;SB=-24.92;SpanningDeletions=0	GT:DP:GQ	1/0:23:19.27	./.	./.
+1	10002963	.	C	G	22.22	.	AF=0.50;AlleleBalance=0.47;DoC=30;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.91;SB=-41.73;SpanningDeletions=0	GT:DP:GQ	0/1:30:33.07	./.	./.
+1	10005008	.	A	T,C	123.78	PASS	AF=1.00;DoC=30;HomopolymerRun=6;MAPQ0=2;NS=1;RMSMAPQ=61.05;SB=-75.45;SpanningDeletions=1	GT:DP:GQ	1/1:27:4.03	0/1:26:3.0	0/0:16:2.0
+1	10006296	.	C	T	42.23	PASS	AF=0.50;AlleleBalance=0.33;DoC=7;HomopolymerRun=0;MAPQ0=11;NS=1;RMSMAPQ=46.62;SB=-0.04;SpanningDeletions=0	GT:DP:GQ	0/1:7:2000000	./.	./.
+1	10023478	.	G	C,A,T	84.23	.	AF=1.00;DoC=27;HomopolymerRun=1;MAPQ0=10;NS=1;RMSMAPQ=42.16;SB=-48.38;SpanningDeletions=0	GT:DP:GQ	1/1:27:4.03	2/2:26:3.0	0/3:16:2.0
+1	10029362	.	T	C	52.22	.	AF=0.50;AlleleBalance=0.52;DoC=44;HomopolymerRun=0;MAPQ0=0;NS=1;RMSMAPQ=81.28;SB=-42.22;SpanningDeletions=0	GT:DP:GQ	./.	1/0:-1:36.62	./.
+1	10042312	.	G	C	31.81	.	AF=0.50;AlleleBalance=0.70;DoC=24;HomopolymerRun=1;MAPQ0=0;NS=1;RMSMAPQ=85.07;SB=0.00;SpanningDeletions=0	GT:DP:GQ	1/0:.:5.85	0/0	0/1:4
+1	10044557	.	C	T	62.22	.	AF=0.50;AlleleBalance=0.68;DoC=31;HomopolymerRun=16;MAPQ0=0;NS=1;RMSMAPQ=85.34;SB=-0.00;SpanningDeletions=0	GT:DP:GQ	./.	./.	0/1:31:15.01
+1	10045603	.	AAAA	A	40.26	PASS	AF=0.50	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10045604	.	A	ACAT	41.26	PASS	AF=0.50	GT:DP:GQ	1/1:14:6.94	0/0:15:7.94	1/0:15:7.94
+1	10048142	.	A	G	126.81	foo	AF=1.00;DoC=36;HomopolymerRun=4;MAPQ0=0;NS=1;RMSMAPQ=82.11;SB=-85.45;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
+1	10048580	.	T	A	72.22	bar;baz	AF=0.50;AlleleBalance=0.69;DoC=33;HomopolymerRun=6;MAPQ0=0;NS=1;RMSMAPQ=84.45;SB=-27.41;SpanningDeletions=0	GT:DP:GQ	0/1:15:7.94	0/0:15:7.94	1/1:15:7.94
diff --git a/public/testdata/oneReadAllInsertion.bam b/public/testdata/oneReadAllInsertion.bam
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diff --git a/public/testdata/oneReadAllInsertion.bam.bai b/public/testdata/oneReadAllInsertion.bam.bai
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index 000000000..051829097
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