diff --git a/example/example.log b/example/example.log
index 194a769..a2fa969 100644
--- a/example/example.log
+++ b/example/example.log
@@ -6,7 +6,7 @@
                       |                             |
                       +-----------------------------+
 
-Copyright (C) 2015-2017 Harvard University.
+Copyright (C) 2015-2018 Harvard University.
 Distributed under the GNU GPLv3+ open source license.
 
 Command line options:
@@ -56,25 +56,25 @@ Setting --histFactor=1.00
 
 BEGINNING STEP 1
 
-Time for step 1: 0.355483
-Time for step 1 MN^2: 0.0182696
+Time for step 1: 0.347481
+Time for step 1 MN^2: 0.0270685
 
-Making hard calls (time: 0.0182719)
+Making hard calls (time: 0.0181408)
 
 
 BEGINNING STEP 2
 
 BATCH 1 OF 1
 Building hash tables
-.................................................................. (time: 0.064307)
+.................................................................. (time: 0.065696)
 
 Phasing samples 1-379
-Time for phasing batch: 0.310312
+Time for phasing batch: 0.309231
 
-Making hard calls (time: 0.0180111)
+Making hard calls (time: 0.0192151)
 
-Time for step 2: 0.392636
-Time for step 2 MN^2: 0.0401966
+Time for step 2: 0.394149
+Time for step 2 MN^2: 0.0408464
 
 
 BEGINNING STEP 3 (PBWT ITERS)
@@ -87,108 +87,108 @@ BEGINNING PBWT ITER 1
 BATCH 1 OF 10
 
 Phasing samples 1-37
-Time for phasing batch: 0.974292
+Time for phasing batch: 0.977095
 
 BATCH 2 OF 10
 
 Phasing samples 38-75
-Time for phasing batch: 0.908252
+Time for phasing batch: 0.898498
 
 BATCH 3 OF 10
 
 Phasing samples 76-113
-Time for phasing batch: 0.932394
+Time for phasing batch: 0.950794
 
 BATCH 4 OF 10
 
 Phasing samples 114-151
-Time for phasing batch: 0.931995
+Time for phasing batch: 0.937661
 
 BATCH 5 OF 10
 
 Phasing samples 152-189
-Time for phasing batch: 0.930893
+Time for phasing batch: 0.909736
 
 BATCH 6 OF 10
 
 Phasing samples 190-227
-Time for phasing batch: 0.92509
+Time for phasing batch: 0.924443
 
 BATCH 7 OF 10
 
 Phasing samples 228-265
-Time for phasing batch: 0.902272
+Time for phasing batch: 0.9072
 
 BATCH 8 OF 10
 
 Phasing samples 266-303
-Time for phasing batch: 0.874671
+Time for phasing batch: 0.926957
 
 BATCH 9 OF 10
 
 Phasing samples 304-341
-Time for phasing batch: 0.899732
+Time for phasing batch: 0.888218
 
 BATCH 10 OF 10
 
 Phasing samples 342-379
-Time for phasing batch: 0.92043
+Time for phasing batch: 0.90299
 
-Time for PBWT iter 1: 9.20008
+Time for PBWT iter 1: 9.22363
 
 BEGINNING PBWT ITER 2
 
 BATCH 1 OF 10
 
 Phasing samples 1-37
-Time for phasing batch: 1.52217
+Time for phasing batch: 1.49903
 
 BATCH 2 OF 10
 
 Phasing samples 38-75
-Time for phasing batch: 1.48203
+Time for phasing batch: 1.4698
 
 BATCH 3 OF 10
 
 Phasing samples 76-113
-Time for phasing batch: 1.51264
+Time for phasing batch: 1.51891
 
 BATCH 4 OF 10
 
 Phasing samples 114-151
-Time for phasing batch: 1.44984
+Time for phasing batch: 1.45062
 
 BATCH 5 OF 10
 
 Phasing samples 152-189
-Time for phasing batch: 1.44166
+Time for phasing batch: 1.42069
 
 BATCH 6 OF 10
 
 Phasing samples 190-227
-Time for phasing batch: 1.48509
+Time for phasing batch: 1.4851
 
 BATCH 7 OF 10
 
 Phasing samples 228-265
-Time for phasing batch: 1.45803
+Time for phasing batch: 1.44716
 
 BATCH 8 OF 10
 
 Phasing samples 266-303
-Time for phasing batch: 1.42937
+Time for phasing batch: 1.49382
 
 BATCH 9 OF 10
 
 Phasing samples 304-341
-Time for phasing batch: 1.45571
+Time for phasing batch: 1.43647
 
 BATCH 10 OF 10
 
 Phasing samples 342-379
-Time for phasing batch: 1.43781
+Time for phasing batch: 1.46241
 
-Time for PBWT iter 2: 14.6745
+Time for PBWT iter 2: 14.6841
 Writing .haps.gz and .sample output
-Time for writing output: 0.275763
-Total elapsed time for analysis = 25.233 sec
+Time for writing output: 0.221324
+Total elapsed time for analysis = 24.9776 sec
diff --git a/example/example_ref.log b/example/example_ref.log
index 22ca2b4..30dffc8 100644
--- a/example/example_ref.log
+++ b/example/example_ref.log
@@ -6,7 +6,7 @@
                       |                             |
                       +-----------------------------+
 
-Copyright (C) 2015-2017 Harvard University.
+Copyright (C) 2015-2018 Harvard University.
 Distributed under the GNU GPLv3+ open source license.
 
 Command line options:
@@ -43,7 +43,7 @@ Average # SNPs per cM:   42
 Number of <=(64-SNP, 1cM) segments: 9
 Average # SNPs per segment: 47
 
-Time for reading input: 5.09883 sec
+Time for reading input: 5.09263 sec
 
 Fraction of heterozygous genotypes: 0.178114
 Typical span of default 100-het history length: 13.44 cM
@@ -59,15 +59,15 @@ PHASING ITER 1 OF 1
 
 Phasing target samples
 ................................................................................
-Time for phasing iter 1: 0.130578
+Time for phasing iter 1: 0.132139
 Writing vcf.gz output to target.phased.vcf.gz
 [W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
 [W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
 [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
 [W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String
 [W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String
-Time for writing output: 0.034054
-Total elapsed time for analysis = 5.26409 sec
+Time for writing output: 0.0356269
+Total elapsed time for analysis = 5.26099 sec
 
 Mean phase confidence of each target individual:
 ID	PHASE_CONFIDENCE
diff --git a/example/example_vcf.log b/example/example_vcf.log
index f34ad3a..e476445 100644
--- a/example/example_vcf.log
+++ b/example/example_vcf.log
@@ -6,7 +6,7 @@
                       |                             |
                       +-----------------------------+
 
-Copyright (C) 2015-2017 Harvard University.
+Copyright (C) 2015-2018 Harvard University.
 Distributed under the GNU GPLv3+ open source license.
 
 Command line options:
@@ -39,25 +39,25 @@ Setting --histFactor=1.00
 
 BEGINNING STEP 1
 
-Time for step 1: 0.26742
-Time for step 1 MN^2: 0.0206005
+Time for step 1: 0.263286
+Time for step 1 MN^2: 0.0227702
 
-Making hard calls (time: 0.0133271)
+Making hard calls (time: 0.018074)
 
 
 BEGINNING STEP 2
 
 BATCH 1 OF 1
 Building hash tables
-.................................................................. (time: 0.0492489)
+.................................................................. (time: 0.0552511)
 
 Phasing samples 1-379
-Time for phasing batch: 0.294299
+Time for phasing batch: 0.292423
 
-Making hard calls (time: 0.014683)
+Making hard calls (time: 0.0192568)
 
-Time for step 2: 0.358237
-Time for step 2 MN^2: 0.038358
+Time for step 2: 0.366938
+Time for step 2 MN^2: 0.0381578
 
 
 BEGINNING STEP 3 (PBWT ITERS)
@@ -70,108 +70,108 @@ BEGINNING PBWT ITER 1
 BATCH 1 OF 10
 
 Phasing samples 1-37
-Time for phasing batch: 1.03369
+Time for phasing batch: 1.02615
 
 BATCH 2 OF 10
 
 Phasing samples 38-75
-Time for phasing batch: 0.99218
+Time for phasing batch: 0.964455
 
 BATCH 3 OF 10
 
 Phasing samples 76-113
-Time for phasing batch: 0.998885
+Time for phasing batch: 0.988999
 
 BATCH 4 OF 10
 
 Phasing samples 114-151
-Time for phasing batch: 0.969435
+Time for phasing batch: 0.978426
 
 BATCH 5 OF 10
 
 Phasing samples 152-189
-Time for phasing batch: 0.932614
+Time for phasing batch: 0.935981
 
 BATCH 6 OF 10
 
 Phasing samples 190-227
-Time for phasing batch: 0.92777
+Time for phasing batch: 0.941438
 
 BATCH 7 OF 10
 
 Phasing samples 228-265
-Time for phasing batch: 0.930884
+Time for phasing batch: 0.935864
 
 BATCH 8 OF 10
 
 Phasing samples 266-303
-Time for phasing batch: 0.924231
+Time for phasing batch: 0.926938
 
 BATCH 9 OF 10
 
 Phasing samples 304-341
-Time for phasing batch: 0.941741
+Time for phasing batch: 0.927558
 
 BATCH 10 OF 10
 
 Phasing samples 342-379
-Time for phasing batch: 0.949201
+Time for phasing batch: 0.932059
 
-Time for PBWT iter 1: 9.60067
+Time for PBWT iter 1: 9.55792
 
 BEGINNING PBWT ITER 2
 
 BATCH 1 OF 10
 
 Phasing samples 1-37
-Time for phasing batch: 1.54516
+Time for phasing batch: 1.56033
 
 BATCH 2 OF 10
 
 Phasing samples 38-75
-Time for phasing batch: 1.53539
+Time for phasing batch: 1.49036
 
 BATCH 3 OF 10
 
 Phasing samples 76-113
-Time for phasing batch: 1.57556
+Time for phasing batch: 1.51976
 
 BATCH 4 OF 10
 
 Phasing samples 114-151
-Time for phasing batch: 1.44469
+Time for phasing batch: 1.48635
 
 BATCH 5 OF 10
 
 Phasing samples 152-189
-Time for phasing batch: 1.43678
+Time for phasing batch: 1.43754
 
 BATCH 6 OF 10
 
 Phasing samples 190-227
-Time for phasing batch: 1.53198
+Time for phasing batch: 1.50166
 
 BATCH 7 OF 10
 
 Phasing samples 228-265
-Time for phasing batch: 1.53109
+Time for phasing batch: 1.48078
 
 BATCH 8 OF 10
 
 Phasing samples 266-303
-Time for phasing batch: 1.4952
+Time for phasing batch: 1.45079
 
 BATCH 9 OF 10
 
 Phasing samples 304-341
-Time for phasing batch: 1.50751
+Time for phasing batch: 1.47995
 
 BATCH 10 OF 10
 
 Phasing samples 342-379
-Time for phasing batch: 1.52464
+Time for phasing batch: 1.42872
 
-Time for PBWT iter 2: 15.128
+Time for PBWT iter 2: 14.8363
 Writing vcf.gz output to phased.vcf.gz
-Time for writing output: 0.154516
-Total elapsed time for analysis = 30.6983 sec
+Time for writing output: 0.176335
+Total elapsed time for analysis = 30.3964 sec
diff --git a/src/EagleMain.cpp b/src/EagleMain.cpp
index 5f10de1..22ed802 100644
--- a/src/EagleMain.cpp
+++ b/src/EagleMain.cpp
@@ -215,7 +215,7 @@ int main(int argc, char *argv[]) {
   cout << "                      +-----------------------------+" << endl;
   cout << endl;
 
-  cout << "Copyright (C) 2015-2017 Harvard University." << endl;
+  cout << "Copyright (C) 2015-2018 Harvard University." << endl;
   cout << "Distributed under the GNU GPLv3+ open source license." << endl << endl;
 
   //cout << "Boost version: " << BOOST_LIB_VERSION << endl;