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: =========

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

import pathlib
import subprocess
import tempfile

import tskit
import msprime


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

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 sys
import tskit
import numpy as np
import numba


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

jeromekelleher

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

import msprime
import tskit
import numba
import numpy as np