meatcar

var User = function () {
  this.loggedIn = false;
};

User.prototype.ensureLogin = function () {
  var dfd;

  if (this.loggedIn) {
    dfd = $.Deferred();
    dfd.resolve();

meatcar

var User = function () {
  this.loggedIn = false;
};

User.prototype.ensureLogin = function () {
  var dfd;

  if (this.loggedIn) {
    dfd = $.Deferred();
    dfd.resolve();

meatcar

git clone git@github.com:charite/jannovar.git
cd jannovar
mvn install 
# SUCCESS

java -jar target/jannovar-0.6-SNAPSHOT.jar --create-refseq
java -jar target/jannovar-0.6-SNAPSHOT.jar -D data/refseq_hg19.ser -U data -g hg19 -V subset_vcfBeta-HG00731-200-37-ASM.vcf
#Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 2
#	at java.lang.String.charAt(String.java:658)
#	at jannovar.annotation.BlockSubstitution.getAnnotationBlockPlusStrand(BlockSubstitution.java:158)

meatcar

##fileformat=VCFv4.1
##INFO=<ID=EFFECT,Number=1,Type=String,Description="variant effect (UTR5,UTR3,intronic,splicing,missense,stoploss,stopgain,startloss,duplication,frameshift-insertion,frameshift-deletion,non-frameshift-deletion,non-frameshift-insertion,synonymous)">
##INFO=<ID=HGVS,Number=1,Type=String,Description="HGVS Nomenclature">
##center=Complete Genomics
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	GS000036397
chr1	11854476	rs1801131	T	.	.	PASS	TYPE=SNP	GT:DP:AD	0/0:79:79,79
chr1	11856378	rs1801133	G	.	.	PASS	TYPE=SNP	GT:DP:AD	0/0:119:119,119
chr1	97547947	rs67376798	T	.	.	PASS	TYPE=SNP	GT:DP:AD	0/0:47:47,47
chr1	97915614	rs3918290	C	.	.	PASS	TYPE=SNP	GT:DP:AD	0/0:53:53,53
chr3	14187449	rs2228001	G	T	.	PASS	EFFECT=MISSENSE;HGVS=XPC:NM_001145769.1:exon16:c.2704C>A:p.Q902K;TYPE=SNP	GT:DP:AD	0/1:38:22,16	

meatcar

Infobright ICE vs IEE

Materials

Run on SSD, 16GB RAM, Intel i7-4770k CPU

Imports are done on an empty database.

largedb contains 87 million pre-imported variants.

meatcar

Infobright ICE vs IEE

Materials

Run on SSD, 16GB RAM, Intel i7-4770k CPU

Imports are done on an empty database.

largedb contains 87 million pre-imported variants.

meatcar

#!/bin/bash

# Script for installing maven 3.2.2 on Centos6
# Run as root.

if [[ $UID -ne 0 ]]
then
  echo "$0 must be run as root"
  exit 1
fi

meatcar

What is Avro?

Parsing the ga4gh API requires you first to understand what is Avro.

Avro is a project that allows you to

• formaly declare and define data structures (schemas in Avro) to be later used in different languages.
• store data in a file
• fetch data from a file

meatcar

public class DrillJDBCTestTrial {
    public static void main(String[] args) throws SQLException, ClassNotFoundException {
        Class.forName("org.apache.drill.jdbc.Driver");
        Connection connection = DriverManager.getConnection("jdbc:drill:zk=local");
        String query = "select N_NAME from dfs.`/home/meatcar/dev/drill/apache-drill-0.7.0/sample-data/nation.parquet`";

        PreparedStatement statement = connection.prepareStatement(query);

        // hangs here
        ResultSet rs = statement.executeQuery();

meatcar

import java.util.HashMap;
import java.util.Map;
import java.util.concurrent.Executor;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;

public class FutureManager {
    Executor executor = Executors.newSingleThreadExecutor();
    Map<String, Future> futures;
    long timeToSleep;