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

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;

meatcar

<?
/////////////////////
// slack2html
// by @levelsio
/////////////////////
//
/////////////////////
// WHAT DOES THIS DO?
/////////////////////
//

meatcar

Camping Checklist

September 11th 2015

• tent (or make sure you have room in someone's)
• sleeping bag (make sure it's rated for the weather)
• therma-rest (keeps you off the ground, warm. Example)
• pillow (optional, just ball up a sweater instead)
• long-sleved shirt or sweater
• long pants
• t-shirts

meatcar

infile = open('test.txt', 'rt')
wordlist = []
while True:
    line = infile.readline()
    if not line:
        break
    answer = line.split('=')
    wordlist.append([answer[0], answer[1][0:-1]])

for word in wordlist:

meatcar

// Version 1
var view = new view({
    initialize: function () {
        this.html(this.template({}));
        this.partview = new PartView({
            el: this.$('.class-part1')
        });
        this.partview2 = new PartView({
            el: this.$('.class-part2')
        });