jeromekelleher

# Efficient computation of the pairwise divergence matrix.
import time
import itertools

import msprime
import tskit
import numba
import numpy as np

jeromekelleher

import sys
import tskit
import numpy as np
import numba


@numba.njit
def _normalise(B):
    K = np.zeros_like(B)
    N = K.shape[0]

jeromekelleher

import sys
import tskit
import numpy as np
import numba


@numba.njit
def sv_tables_init(parent_array):
    # This is an implementation of Schieber and Vishkin's nearest common ancestor
    # algorithm from TAOCP volume 4A, pg.164-167 [K11]_. Preprocesses the

jeromekelleher

import pathlib
import subprocess
import tempfile

import tskit
import msprime


def draw_transitioning_tree(tree, filename, edge_colours):
    tree.draw(

jeromekelleher

import pathlib
import subprocess

import msprime


def draw_partial_tree(tables, edges, filename):
    tables.edges.clear()
    for edge in edges:
        tables.edges.add_row(*edge)

jeromekelleher

(gdb) run scripts/download_data.py
Starting program: /usr/bin/python scripts/download_data.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Cleaning out directory '/home/jk/work/github/server/ga4gh-downloaded-data/dataset1/reads/low-coverage'
Downloading index for 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam'
[M::test_and_fetch] downloading file 'ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.bai' to local directory
Writing 'HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam'
*** buffer overflow detected ***: /usr/bin/python terminated
======= Backtrace: =========