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commit 8c760af66385fd1f0d45db7fbf8f539936dac955 Author: Dylan Aïssi <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/eagle.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
