IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.
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#pragma once | |
#include <stdint.h> | |
#include <stdlib.h> | |
#include <string.h> | |
#include <type_traits> | |
typedef uint32_t khint_t; | |
typedef khint_t khiter_t; |
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chmod a+x vcfsort.sh | |
vcfsort.sh trio.trim.vep.vcf.gz |
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#include <stdio.h> | |
#include <string.h> | |
#include <stdlib.h> | |
#include <htslib/sam.h> | |
int main(int argc, char *argv[]){ | |
samFile *fp_in = hts_open(argv[1],"r"); //open bam file | |
bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //read header | |
bam1_t *aln = bam_init1(); //initialize an alignment |
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/* | |
For any 1<k<=64, let mask=(1<<k)-1. hash_64() is a bijection on [0,1<<k), which means | |
hash_64(x, mask)==hash_64(y, mask) if and only if x==y. hash_64i() is the inversion of | |
hash_64(): hash_64i(hash_64(x, mask), mask) == hash_64(hash_64i(x, mask), mask) == x. | |
*/ | |
// Thomas Wang's integer hash functions. See <https://gist.github.com/lh3/59882d6b96166dfc3d8d> for a snapshot. | |
uint64_t hash_64(uint64_t key, uint64_t mask) | |
{ | |
key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1; |
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one <- seq(1:10) | |
two <- rnorm(10) | |
three <- runif(10, 1, 2) | |
four <- -10:-1 | |
df <- data.frame(one, two, three) | |
df2 <- data.frame(one, two, three, four) | |
str(df) |
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# -*- coding: utf-8 -*- | |
def kmer(sequence,k): | |
length=len(sequence) | |
#if the kmer size if greater than the lenght of the sequene | |
if k>=length: | |
print "You specified a kmer size, which if greater or equal to the length of the sequence" | |
return | |
stepsize=k-1 | |
i=0 | |
kmers=[] |
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git clean -xfd | |
git submodule foreach --recursive git clean -xfd | |
git reset --hard | |
git submodule foreach --recursive git reset --hard | |
git submodule update --init --recursive |
SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please extend with additional/faster/better solutions via a pull request!
BWA mapping (using piping for minimal disk I/O)
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library(ggbio) | |
library(grid) | |
library(gridExtra) | |
library(plyr) | |
library(GenomicRanges) | |
library(qgraph) | |
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) | |
{ | |
require(grid) |