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  {
    "url": "https://api.github.com/repos/hail-is/hail/pulls/3656",
    "id": 190363631,
    "node_id": "MDExOlB1bGxSZXF1ZXN0MTkwMzYzNjMx",
    "html_url": "https://github.com/hail-is/hail/pull/3656",
    "diff_url": "https://github.com/hail-is/hail/pull/3656.diff",
    "patch_url": "https://github.com/hail-is/hail/pull/3656.patch",
    "issue_url": "https://api.github.com/repos/hail-is/hail/issues/3656",
    "number": 3656,
    "state": "open",

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2 dking@wmb16-359 # make clean ; make
rm -rf _build
jbuilder build @install
      ocamlc common/iron_common.{cmi,cmo,cmt}
      ocamlc hg/iron_hg.{cmi,cmo,cmt}
      ocamlc client/iron_client.{cmi,cmo,cmt}
      ocamlc public/iron.{cmi,cmo,cmt}
      ocamlc patdiff4/lib/pdiff4.{cmi,cmo,cmt}
      ocamlc obligations/iron_obligations.{cmi,cmo,cmt}
      ocamlc server/iron_server.{cmi,cmo,cmt}

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From 9cfae509b03a69de267fe58f15e1e902468f3bbf Mon Sep 17 00:00:00 2001
From: Daniel King <[email protected]>
Date: Mon, 8 May 2017 11:12:30 -0400
Subject: [PATCH] add timing tests

---
 .../is/hail/variant/GenericDatasetSuite.scala      | 44 ++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/src/test/scala/is/hail/variant/GenericDatasetSuite.scala b/src/test/scala/is/hail/variant/GenericDatasetSuite.scala

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From 2e04cc3fdc3d6a9ac2531b905c93a4fe7c504ea5 Mon Sep 17 00:00:00 2001
From: Daniel King <[email protected]>
Date: Fri, 24 Mar 2017 21:43:00 -0400
Subject: [PATCH] use breeze non-natives

---
 build.gradle | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/build.gradle b/build.gradle

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#include <x86intrin.h>
#include <avxintrin.h>
#include <avx2intrin.h>
#include <popcntintrin.h>
#include <stdint.h>
#include <stdio.h>

__m256i allones = { 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF };
__m256i rightAllele = { 0x5555555555555555, 0x5555555555555555, 0x5555555555555555, 0x5555555555555555 };

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hail: info: running: read -i file:///mnt/lustre/mzekavat/MESA_VIRGO/rawVDS/raw_MESA_VIRGO.vds
[Stage 1:======================================================>(159 + 1) / 160]hail: info: running: filtervariants expr -c 'v.contig == "X"' --keep
hail: info: running: filtersamples expr -c '"^NW" ~ s.id' --keep
hail: info: running: filtersamples list --remove -i file:///mnt/lustre/mzekavat/MESA_VIRGO/MESA_ONLY/QCed_VDS/MESA_badSamples_Cvg30_Contam3.txt
hail: info: running: filtervariants intervals -i file:///mnt/lustre/aganna/LCR.interval_list --remove
hail: info: running: filtervariants expr -c va.pass --keep
hail: info: running: filtergenotypes -c '(g.ad[0] + g.ad[1]) / g.dp < 0.9 || (g.isHomRef && (g.ad[0] / g.dp < 0.9 || g.gq < 20)) || (g.isHet && (g.ad[1] / g.dp < 0.20 || g.pl[0] < 20)) || (g.isHomVar && (g.ad[1] / g.dp < 0.9 || g.pl[0] < 20)) || g.dp > 200' --remove
hail: info: running: variantqc
hail: info: running: filtervariants expr -c '((va.info.QD > 3 && v.altAllele.isIndel) || (va.info.QD > 2 && v.alt

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{-# LANGUAGE DeriveFunctor, FlexibleInstances, OverlappingInstances #-}
module Main where

-- Standard Library imports

import Control.Applicative (Applicative, (<$>), (<*>), pure, liftA2)
import Control.Monad
import Control.Monad.Identity
import Control.Monad.Free (Free(..), iterM, liftF)

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class ESLogger implements ILogger {
  public ESLogger(ElasticSearchConfig esc) {
    //...
  }
  
  public static ILogger fromConfig(Optional<ElasticSearchConfig> esc) {
    return esc
      .map(ESLogger::new)
      .orElse(ILogger.zero());
  }

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data Criteria = Criteria (Conjunction (Disjunction Term)) (Disjunction (Conjunction Term))
              deriving Show

data Term = Term String
          deriving Show

data Conjunction a = Conjunction [a]
                   deriving Show

data Disjunction a = Disjunction [a]