new truncated test data set

TestData/65283_chr22_20to30MB.log

@@ -0,0 +1,69 @@
+Version:	1.2.9
+Arguments Used:
+-b	65283_treat_rep1.chr22.20to30MB.bam
+-i	65283_treat_rep1.chr22.20to30MB.bam.bai
+-g	hg19.chr22.genome
+--window	100000
+-o	65283_chr22_20to30MB
+-p	true
+-u	20
+-l	10
+Fragment Expectation Maximum Done
+Mean	50.0	StdDevs	20.0
+Mean	182.17175917152832	StdDevs	40.68592596649732
+Mean	359.5832398292082	StdDevs	41.09125945615911
+Mean	527.5501422573168	StdDevs	48.44333621164874
+ScalingFactor	0.215267
+Training Regions found and Zscore regions for exclusion found
+Training Fragment Pileup completed
+Kmeans Model:
+HMM with 3 state(s)
+
+State 0
+  Pi: 0.3333333333333333
+  Aij: 0.333 0.333 0.333
+  Opdf: Multi-variate Gaussian distribution --- Mean: [ 0.372 0.676 0.286 0.081 ]
+
+State 1
+  Pi: 0.3333333333333333
+  Aij: 0.333 0.333 0.333
+  Opdf: Multi-variate Gaussian distribution --- Mean: [ 1.341 2.996 1.291 0.3 ]
+
+State 2
+  Pi: 0.3333333333333333
+  Aij: 0.333 0.333 0.333
+  Opdf: Multi-variate Gaussian distribution --- Mean: [ 3.777 6.505 4.572 2.042 ]
+
+Model created and refined. See 65283_chr22_20to30MB.model
+Model:
+HMM with 3 state(s)
+
+State 0
+  Pi: 0.3333333333333333
+  Aij: 0.942 0.05 0.008
+  Opdf: Multi-variate Gaussian distribution --- Mean: [ 0 0 0 0 ]
+
+State 1
+  Pi: 0.3333333333333333
+  Aij: 0.036 0.948 0.016
+  Opdf: Multi-variate Gaussian distribution --- Mean: [ 1.195 2.339 0.055 0 ]
+
+State 2
+  Pi: 0.3333333333333333
+  Aij: 0.006 0.013 0.981
+  Opdf: Multi-variate Gaussian distribution --- Mean: [ 1.347 2.871 2.253 0.666 ]
+
+Genome split and subtracted masked regions
+0 round viterbi done
+50 round viterbi done
+100 round viterbi done
+150 round viterbi done
+200 round viterbi done
+250 round viterbi done
+300 round viterbi done
+350 round viterbi done
+400 round viterbi done
+450 round viterbi done
+500 round viterbi done
+513 round viterbi done
+Total time (seconds)= 	2435

TestData/65283_chr22_20to30MB_peaks.gappedPeak

@@ -0,0 +1,23 @@
+chr22	20020520	20022460	Peak_23	.	.	20020540	20022340	255,0,0	3	1,1800,1	0,20,1939	43.0	-1	-1
+chr22	20079670	20080570	Peak_69	.	.	20079700	20080560	255,0,0	3	1,860,1	0,30,899	40.0	-1	-1
+chr22	20116700	20117700	Peak_101	.	.	20116780	20117530	255,0,0	3	1,750,1	0,80,999	45.0	-1	-1
+chr22	20858410	20859650	Peak_610	.	.	20858500	20859640	255,0,0	3	1,1140,1	0,90,1239	44.0	-1	-1
+chr22	20915930	20918650	Peak_647	.	.	20916710	20918320	255,0,0	3	1,1610,1	0,780,2719	51.0	-1	-1
+chr22	20981770	20982640	Peak_694	.	.	20981840	20982560	255,0,0	3	1,720,1	0,70,869	36.0	-1	-1
+chr22	21001060	21002680	Peak_709	.	.	21001110	21002570	255,0,0	3	1,1460,1	0,50,1619	30.0	-1	-1
+chr22	21641400	21642660	Peak_867	.	.	21641540	21642520	255,0,0	3	1,980,1	0,140,1259	41.0	-1	-1
+chr22	21665380	21667170	Peak_882	.	.	21665770	21666580	255,0,0	3	1,810,1	0,390,1789	31.0	-1	-1
+chr22	22927280	22930170	Peak_1756	.	.	22927720	22929910	255,0,0	3	1,2190,1	0,440,2889	53.0	-1	-1
+chr22	23838670	23839700	Peak_2440	.	.	23838690	23839410	255,0,0	3	1,720,1	0,20,1029	39.0	-1	-1
+chr22	23857620	23858550	Peak_2452	.	.	23857680	23858280	255,0,0	3	1,600,1	0,60,929	33.0	-1	-1
+chr22	23913250	23914450	Peak_2496	.	.	23913400	23914150	255,0,0	3	1,750,1	0,150,1199	30.0	-1	-1
+chr22	24270710	24272020	Peak_2723	.	.	24270790	24271880	255,0,0	3	1,1090,1	0,80,1309	30.0	-1	-1
+chr22	24432970	24435880	Peak_2823	.	.	24433080	24435550	255,0,0	3	1,2470,1	0,110,2909	31.0	-1	-1
+chr22	24607110	24608370	Peak_2960	.	.	24607120	24608240	255,0,0	3	1,1120,1	0,10,1259	32.0	-1	-1
+chr22	25404540	25407420	Peak_3516	.	.	25404620	25407310	255,0,0	3	1,2690,1	0,80,2879	34.0	-1	-1
+chr22	27919060	27920140	Peak_5590	.	.	27919210	27920120	255,0,0	3	1,910,1	0,150,1079	44.0	-1	-1
+chr22	28741380	28742040	Peak_6010	.	.	28741540	28742010	255,0,0	3	1,470,1	0,160,659	51.0	-1	-1
+chr22	28800220	28801520	Peak_6054	.	.	28800290	28801170	255,0,0	3	1,880,1	0,70,1299	31.0	-1	-1
+chr22	29267340	29269170	Peak_6400	.	.	29267390	29269110	255,0,0	3	1,1720,1	0,50,1829	30.0	-1	-1
+chr22	29602890	29605150	Peak_6644	.	.	29603050	29605090	255,0,0	3	1,2040,1	0,160,2259	53.0	-1	-1
+chr22	29837620	29838740	Peak_6819	.	.	29837700	29838720	255,0,0	3	1,1020,1	0,80,1119	30.0	-1	-1

TestData/65283_chr22_20to30MB_summits.bed

@@ -0,0 +1,23 @@
+chr22	20021044	20021045	Peak_23	43.0
+chr22	20080106	20080107	Peak_69	40.0
+chr22	20117305	20117306	Peak_101	45.0
+chr22	20858852	20858853	Peak_610	44.0
+chr22	20917322	20917323	Peak_647	51.0
+chr22	20982201	20982202	Peak_694	36.0
+chr22	21002183	21002184	Peak_709	30.0
+chr22	21642141	21642142	Peak_867	41.0
+chr22	21666264	21666265	Peak_882	31.0
+chr22	22928830	22928831	Peak_1756	53.0
+chr22	23839286	23839287	Peak_2440	39.0
+chr22	23857874	23857875	Peak_2452	33.0
+chr22	23913989	23913990	Peak_2496	30.0
+chr22	24270838	24270839	Peak_2723	30.0
+chr22	24434261	24434262	Peak_2823	31.0
+chr22	24607544	24607545	Peak_2960	32.0
+chr22	25405410	25405411	Peak_3516	34.0
+chr22	27919489	27919490	Peak_5590	44.0
+chr22	28741938	28741939	Peak_6010	51.0
+chr22	28800628	28800629	Peak_6054	31.0
+chr22	29268019	29268020	Peak_6400	30.0
+chr22	29603511	29603512	Peak_6644	53.0
+chr22	29838361	29838362	Peak_6819	30.0