| import os | |
| import stats | |
| import hts | |
| import plotly | |
| import strformat | |
| import bpbiopkg/pedfile | |
| #[ | |
| look at allele balance on mitochondrial chromosome. | |
| this only plots sites for each sample that have an allele balance (alt / ref + alt) between 0.01 and 0.99. |
| type Signal* = object | |
| left*: uint32 | |
| right*: uint32 | |
| left_exact* {.bitsize: 1.}: uint32 | |
| right_exact* {.bitsize: 1.}: uint32 | |
| when defined(debug): | |
| name*: string | |
| proc makeSignal(): Signal = | |
| result.left_exact = 1'u32 |
| import hts | |
| import strformat | |
| import os | |
| import osproc | |
| import tables | |
| var | |
| vcf_path = commandLineParams()[0] | |
| fasta_path = commandLineParams()[1] | |
| vcf: VCF |
| {.emit:""" | |
| #define bam_get_qual(b) ((b)->data + ((b)->core.n_cigar<<2) + (b)->core.l_qname + (((b)->core.l_qseq + 1)>>1)) | |
| """.} | |
| proc bam_get_qual*(b: ptr bam1_t): ptr uint8 {.importc, nodecl.} |
| # http://docs.aws.amazon.com/batch/latest/userguide/create-batch-ami.html | |
| sudo yum update | |
| sudo yum install -y grub | |
| sudo yum install -y ecs-init | |
| sudo reboot now | |
| sudo stop ecs | |
| sudo rm -rf /var/lib/ecs/data/ecs_agent_data.json | |
| sudo -E su |
| import numpy as np | |
| from matplotlib import pyplot as plt | |
| from matplotlib import gridspec | |
| import seaborn as sns | |
| sns.set_style('white') | |
| def geneplot(exons, patho_variants, population_variants=None, constraint=None, | |
| density=None, | |
| opts={'constraint_color': (0.7, 0.7, 0.7), |
| package bit_test | |
| import ( | |
| "math/big" | |
| "testing" | |
| ) | |
| func BenchmarkUint64(b *testing.B) { | |
| for i := 0; i < b.N; i++ { | |
| var x uint64 |
| apt-get update | |
| apt-get -qy install libcurl4-openssl-dev curl cmake make build-essential libbz2-dev lzma-dev liblzma-dev git \ | |
| python-dev | |
| mkdir -p /home/ubuntu | |
| cd /home/ubuntu | |
| git clone --depth 1 http://root.cern.ch/git/root.git | |
| mkdir root/ibuild | |
| cd root/ibuild | |
| cmake -D x11=OFF ../ | |
| make -j4 install |
| from scipy.stats import chisquare | |
| import sys | |
| def cnrand(counts): | |
| """ | |
| cnrand will return the chisquare p-value of the observed distribution | |
| of copy-number genomes **of the same CN with 0...n copies of H47R | |
| # test 4-copy genomes (0 ... 4) | |
| # 1 0 copy, 1 3-copy and 1 4-copy |
Last updated: Feb. 8, 2017
CRAM format encodes genomic alignments to a reference.
It has better lossless (and optional lossy) compression compared to existing BAM format. It is also
becoming more widely used. We propose the addition of a CRAM Reader to biogo/hts
under hts/cram.