mfcovington

A01	800	810

mfcovington

Example from https://github.com/blog/1375%0A-task-lists-in-gfm-issues-pulls-comments:

• a task list item
• list syntax required
• normal formatting, @mentions, #1234 refs
• incomplete
• completed

mfcovington

[
    {
        "title"   : "A modern ampelography: a genetic basis for leaf shape and venation patterning in grape",
        "journal" : "Plant Physiology",
        "year"    : "2014",
        "authors" : "Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya M, Prins B, Li L, Myles S, Sinha NR",
        "pubmed"  : "24285849",
        "pdf"     : "https://github.com/mfcovington/mfcovington.github.com/blob/master/resources/pdf/Plant Physiol.-2014-Chitwood-259-72.pdf?raw=true",
        "si"      : ""

mfcovington

#!/usr/bin/env perl
# Mike Covington
# created: 2014-05-23
#
# Description:
#
use strict;
use warnings;
use autodie;
use feature 'say';

mfcovington

library(ggplot2)
library(reshape)

par1 <- "M82"
par2 <- "PEN"

boundary.files <- list.files(pattern = "\\.boundaries$")

for (file in boundary.files) {
  bounds <- read.table(file)

mfcovington

Links for Variant Calling iPlant Workshop

IGV (Integrative Genomics Viewer)

Variant Calling with SAMtools/BCFtools

• 'Find SNPS - mpileup' in Discovery Environment: basic and easy
• 'Calling SNPs INDELs with SAMtools BCFtools' in Discovery Environment: many parameters and options available
• Command Line: total control

mfcovington

@benkasminbullock: Thanks for the question. Log::Reproducible takes a look at @ARGV to create an archive. Any module-specific options/args (--repronote, --reprodir) should get removed from @ARGV before @ARGV is accessed by the script that calls the reproduce() function. @ARGV is then used by the script as it would normally have been.

You bring up a good point. What if some other module tries to access @ARGV before Log::Reproducible? I was able to 'break' it by using another module that messed with @ARGV in a BEGIN block (even if the module was called after reproduce()). I could fix this with the following (as long as it is placed early enough in the code):

use Log::Reproducible;
BEGIN { reproduce(); }

Alternatively, I could fix it by placing the reproduce(); call inside an import subroutine in the module. This would prevent one from setting a script-level archive directory. However, I could restore this functionality by

mfcovington

#!/usr/bin/env perl
use strict;
use warnings;
use List::Util 'max';
use Benchmark 'cmpthese';

my $count = 100_000;

my %test_ranges = (
    10  => 20,

mfcovington

Left align	Right align	Center align
This	This	This
column	column	column
will	will	will
be	be	be
left	right	center
aligned	aligned	aligned

mfcovington

library(ggplot2)
df <- data.frame(x = rnorm(100000), y = rnorm(100000))
df.sub <- subset(df, x * y < 2.5 & x * y > -2.5)
ggplot(df.sub, aes(x, y, color = x * y)) +
  geom_point(alpha = I(0.5)) +
  scale_color_gradientn(colours = rainbow(10), limits=c(-2.5, 2.5)) +
  theme(aspect.ratio     = 1,
        panel.background = element_rect(fill = "black"),
        panel.grid       = element_blank(),
        plot.background  = element_rect(fill = "black"),