[med-svn] [eagle] 01/04: New upstream version 2.3.5
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Wed Aug 16 21:00:05 UTC 2017
This is an automated email from the git hooks/post-receive script.
bob.dybian-guest pushed a commit to branch master
in repository eagle.
commit 8c760af66385fd1f0d45db7fbf8f539936dac955
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Wed Aug 16 22:50:09 2017 +0200
New upstream version 2.3.5
---
example/example.log | 68 +++++++++++++++++++++----------------------
example/example_ref.log | 10 +++----
example/example_vcf.log | 68 +++++++++++++++++++++----------------------
example/phased.vcf.gz | Bin 200384 -> 200383 bytes
example/target.phased.vcf.gz | Bin 21053 -> 21053 bytes
src/Eagle.cpp | 2 +-
src/Version.hpp | 4 +--
7 files changed, 76 insertions(+), 76 deletions(-)
diff --git a/example/example.log b/example/example.log
index a85bbc2..a916d76 100644
--- a/example/example.log
+++ b/example/example.log
@@ -1,7 +1,7 @@
+-----------------------------+
| |
- | Eagle v2.3.4 |
- | June 5, 2017 |
+ | Eagle v2.3.5 |
+ | August 2, 2017 |
| Po-Ru Loh |
| |
+-----------------------------+
@@ -56,25 +56,25 @@ Setting --histFactor=1.00
BEGINNING STEP 1
-Time for step 1: 0.372298
-Time for step 1 MN^2: 0.0234743
+Time for step 1: 0.373437
+Time for step 1 MN^2: 0.023717
-Making hard calls (time: 0.0283618)
+Making hard calls (time: 0.028342)
BEGINNING STEP 2
BATCH 1 OF 1
Building hash tables
-.................................................................. (time: 0.0564198)
+.................................................................. (time: 0.050245)
Phasing samples 1-379
-Time for phasing batch: 0.455953
+Time for phasing batch: 0.433878
-Making hard calls (time: 0.0308828)
+Making hard calls (time: 0.030308)
-Time for step 2: 0.543273
-Time for step 2 MN^2: 0.060238
+Time for step 2: 0.514443
+Time for step 2 MN^2: 0.0593926
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: 1.79289
+Time for phasing batch: 1.75117
BATCH 2 OF 10
Phasing samples 38-75
-Time for phasing batch: 1.63213
+Time for phasing batch: 1.58165
BATCH 3 OF 10
Phasing samples 76-113
-Time for phasing batch: 1.72728
+Time for phasing batch: 1.68042
BATCH 4 OF 10
Phasing samples 114-151
-Time for phasing batch: 1.67067
+Time for phasing batch: 1.6039
BATCH 5 OF 10
Phasing samples 152-189
-Time for phasing batch: 1.6183
+Time for phasing batch: 1.59436
BATCH 6 OF 10
Phasing samples 190-227
-Time for phasing batch: 1.64558
+Time for phasing batch: 1.64487
BATCH 7 OF 10
Phasing samples 228-265
-Time for phasing batch: 1.66745
+Time for phasing batch: 1.60414
BATCH 8 OF 10
Phasing samples 266-303
-Time for phasing batch: 1.5854
+Time for phasing batch: 1.51987
BATCH 9 OF 10
Phasing samples 304-341
-Time for phasing batch: 1.65665
+Time for phasing batch: 1.56367
BATCH 10 OF 10
Phasing samples 342-379
-Time for phasing batch: 1.65564
+Time for phasing batch: 1.5805
-Time for PBWT iter 1: 16.652
+Time for PBWT iter 1: 16.1246
BEGINNING PBWT ITER 2
BATCH 1 OF 10
Phasing samples 1-37
-Time for phasing batch: 2.78407
+Time for phasing batch: 2.70429
BATCH 2 OF 10
Phasing samples 38-75
-Time for phasing batch: 2.63331
+Time for phasing batch: 2.5743
BATCH 3 OF 10
Phasing samples 76-113
-Time for phasing batch: 2.79219
+Time for phasing batch: 2.70542
BATCH 4 OF 10
Phasing samples 114-151
-Time for phasing batch: 2.63535
+Time for phasing batch: 2.56365
BATCH 5 OF 10
Phasing samples 152-189
-Time for phasing batch: 2.63604
+Time for phasing batch: 2.50088
BATCH 6 OF 10
Phasing samples 190-227
-Time for phasing batch: 2.73293
+Time for phasing batch: 2.58336
BATCH 7 OF 10
Phasing samples 228-265
-Time for phasing batch: 2.68814
+Time for phasing batch: 2.59174
BATCH 8 OF 10
Phasing samples 266-303
-Time for phasing batch: 2.52878
+Time for phasing batch: 2.47758
BATCH 9 OF 10
Phasing samples 304-341
-Time for phasing batch: 2.63756
+Time for phasing batch: 2.48646
BATCH 10 OF 10
Phasing samples 342-379
-Time for phasing batch: 2.67104
+Time for phasing batch: 2.57226
-Time for PBWT iter 2: 26.7394
+Time for PBWT iter 2: 25.76
Writing .haps.gz and .sample output
-Time for writing output: 0.40393
-Total elapsed time for analysis = 44.9436 sec
+Time for writing output: 0.306937
+Total elapsed time for analysis = 43.2534 sec
diff --git a/example/example_ref.log b/example/example_ref.log
index 6eb6a7f..bb3c432 100644
--- a/example/example_ref.log
+++ b/example/example_ref.log
@@ -1,7 +1,7 @@
+-----------------------------+
| |
- | Eagle v2.3.4 |
- | June 5, 2017 |
+ | Eagle v2.3.5 |
+ | August 2, 2017 |
| Po-Ru Loh |
| |
+-----------------------------+
@@ -56,15 +56,15 @@ PHASING ITER 1 OF 1
Phasing target samples
................................................................................
-Time for phasing iter 1: 0.259136
+Time for phasing iter 1: 0.236665
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: 0.0443978
-Total elapsed time for analysis = 10.1217 sec
+Time for writing output: 0.028465
+Total elapsed time for analysis = 9.34482 sec
Mean phase confidence of each target individual:
ID PHASE_CONFIDENCE
diff --git a/example/example_vcf.log b/example/example_vcf.log
index a8177cf..c901b3c 100644
--- a/example/example_vcf.log
+++ b/example/example_vcf.log
@@ -1,7 +1,7 @@
+-----------------------------+
| |
- | Eagle v2.3.4 |
- | June 5, 2017 |
+ | Eagle v2.3.5 |
+ | August 2, 2017 |
| Po-Ru Loh |
| |
+-----------------------------+
@@ -39,25 +39,25 @@ Setting --histFactor=1.00
BEGINNING STEP 1
-Time for step 1: 0.382344
-Time for step 1 MN^2: 0.024531
+Time for step 1: 0.37492
+Time for step 1 MN^2: 0.0236487
-Making hard calls (time: 0.0279789)
+Making hard calls (time: 0.02865)
BEGINNING STEP 2
BATCH 1 OF 1
Building hash tables
-.................................................................. (time: 0.0512731)
+.................................................................. (time: 0.0538409)
Phasing samples 1-379
-Time for phasing batch: 0.44787
+Time for phasing batch: 0.435353
-Making hard calls (time: 0.0295429)
+Making hard calls (time: 0.0303631)
-Time for step 2: 0.528698
-Time for step 2 MN^2: 0.0594785
+Time for step 2: 0.519568
+Time for step 2 MN^2: 0.0592469
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: 1.78389
+Time for phasing batch: 1.79524
BATCH 2 OF 10
Phasing samples 38-75
-Time for phasing batch: 1.66108
+Time for phasing batch: 1.61659
BATCH 3 OF 10
Phasing samples 76-113
-Time for phasing batch: 1.72659
+Time for phasing batch: 1.70906
BATCH 4 OF 10
Phasing samples 114-151
-Time for phasing batch: 1.6426
+Time for phasing batch: 1.63612
BATCH 5 OF 10
Phasing samples 152-189
-Time for phasing batch: 1.629
+Time for phasing batch: 1.60907
BATCH 6 OF 10
Phasing samples 190-227
-Time for phasing batch: 1.63717
+Time for phasing batch: 1.65953
BATCH 7 OF 10
Phasing samples 228-265
-Time for phasing batch: 1.66667
+Time for phasing batch: 1.657
BATCH 8 OF 10
Phasing samples 266-303
-Time for phasing batch: 1.5801
+Time for phasing batch: 1.59278
BATCH 9 OF 10
Phasing samples 304-341
-Time for phasing batch: 1.60071
+Time for phasing batch: 1.61661
BATCH 10 OF 10
Phasing samples 342-379
-Time for phasing batch: 1.60565
+Time for phasing batch: 1.59879
-Time for PBWT iter 1: 16.5335
+Time for PBWT iter 1: 16.4908
BEGINNING PBWT ITER 2
BATCH 1 OF 10
Phasing samples 1-37
-Time for phasing batch: 2.80026
+Time for phasing batch: 2.72667
BATCH 2 OF 10
Phasing samples 38-75
-Time for phasing batch: 2.68277
+Time for phasing batch: 2.55292
BATCH 3 OF 10
Phasing samples 76-113
-Time for phasing batch: 2.77932
+Time for phasing batch: 2.68511
BATCH 4 OF 10
Phasing samples 114-151
-Time for phasing batch: 2.58917
+Time for phasing batch: 2.57207
BATCH 5 OF 10
Phasing samples 152-189
-Time for phasing batch: 2.58681
+Time for phasing batch: 2.51047
BATCH 6 OF 10
Phasing samples 190-227
-Time for phasing batch: 2.64623
+Time for phasing batch: 2.6027
BATCH 7 OF 10
Phasing samples 228-265
-Time for phasing batch: 2.67757
+Time for phasing batch: 2.619
BATCH 8 OF 10
Phasing samples 266-303
-Time for phasing batch: 2.53453
+Time for phasing batch: 2.47177
BATCH 9 OF 10
Phasing samples 304-341
-Time for phasing batch: 2.59236
+Time for phasing batch: 2.52629
BATCH 10 OF 10
Phasing samples 342-379
-Time for phasing batch: 2.606
+Time for phasing batch: 2.5489
-Time for PBWT iter 2: 26.4951
+Time for PBWT iter 2: 25.8159
Writing vcf.gz output to phased.vcf.gz
-Time for writing output: 0.362386
-Total elapsed time for analysis = 54.0173 sec
+Time for writing output: 0.316302
+Total elapsed time for analysis = 53.0844 sec
diff --git a/example/phased.vcf.gz b/example/phased.vcf.gz
index 6e80a7c..67ee350 100644
Binary files a/example/phased.vcf.gz and b/example/phased.vcf.gz differ
diff --git a/example/target.phased.vcf.gz b/example/target.phased.vcf.gz
index 8120c71..81664e0 100644
Binary files a/example/target.phased.vcf.gz and b/example/target.phased.vcf.gz differ
diff --git a/src/Eagle.cpp b/src/Eagle.cpp
index dfe1b80..6e185b5 100644
--- a/src/Eagle.cpp
+++ b/src/Eagle.cpp
@@ -3333,7 +3333,7 @@ namespace EAGLE {
}
m64j++;
- if ((m64j&63) == seg64cMvecs[m64j/64].size())
+ if (m64j != Mseg64*64 && (m64j&63) == seg64cMvecs[m64j/64].size())
m64j = (m64j + 64ULL) & ~63ULL; // move to next segment
}
diff --git a/src/Version.hpp b/src/Version.hpp
index 4518d27..07ad47e 100644
--- a/src/Version.hpp
+++ b/src/Version.hpp
@@ -19,7 +19,7 @@
#ifndef VERSION_HPP
#define VERSION_HPP
-const char EAGLE_VERSION[] = "2.3.4";
-const char EAGLE_VERSION_DATE[] = "June 5, 2017";
+const char EAGLE_VERSION[] = "2.3.5";
+const char EAGLE_VERSION_DATE[] = "August 2, 2017";
#endif
--
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