This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
// Helper functions | |
// A list consists of any number of 'rule', separated by separator, and the last one is optional. | |
const list = (rule, separator) => seq(rule, repeat(seq(separator, rule))) | |
const NL = choice("\r\n", "\r", "\n") | |
const NLOPT = prec(-1, repeat(NL)) | |
// in ascending order of precedence | |
const operator_table = [ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
function create_confetti() | |
v=1.4 --initial velocity | |
size=40 | |
-- the center of the confetti | |
balloon_x=40 | |
balloon_y=40 | |
for i=1,100 do | |
local r=rnd(size) -- this is how far out from the center it starts | |
local n=rnd(1) -- this is the angle it goes at | |
confetti[i] = { |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
package locale | |
import ( | |
"bufio" | |
"fmt" | |
"io" | |
"regexp" | |
"strconv" | |
"strings" | |
"unicode/utf8" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
package main | |
import ( | |
"encoding/csv" | |
"fmt" | |
"io" | |
"log" | |
"os" | |
) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/env python3 | |
from Bio import SeqIO | |
from collections import defaultdict | |
import time | |
M = 7 | |
Q = 10 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
for fastq in $SAMPLE_NAME*.fastq.gz; do | |
zcat $fastq \ | |
| awk '/Y/' \ | |
`basename $fastq .gz` >filtered_ | |
done |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#include <iostream> | |
#include <vector> | |
#include <random> | |
std::random_device rd; | |
std::mt19937 rng(rd()); | |
const int ITERATIONS = 300; | |
const int IN_SIZE = 1000000; |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
# Normal layout of a healthy read-pair. | |
fragment ======================================== | |
fragment + adaptors ~~~========================================~~~ | |
SE read ---------> | |
PE reads R1---------> <---------R2 | |
unknown gap .................... |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
username="MYUSERNAME" | |
origPort="80" | |
midlPort="38080" | |
destPort="80" | |
midlHost="MYMIDDLEMAN" | |
destHost="MYDESTINATION" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
qsub -cwd -N "u-H3MHT" -pe threads 8 -V -S /bin/bash <<'__FASTQ__' | |
set -x -e -o pipefail | |
cd "/net/glados/solexa_data/150109_NS500372_0058_AH3MHTBGXX" | |
bcl2fastq \ | |
--input-dir "/net/glados/solexa_data/150109_NS500372_0058_AH3MHTBGXX/Data/Intensities/BaseCalls" \ | |
--use-bases-mask "y36,I6n,y36" \ | |
--output-dir "/net/glados/solexa_data/150109_NS500372_0058_AH3MHTBGXX/fastq" \ |
NewerOlder