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Shaun Jackman sjackman

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sjackman / bwtdisk-0.9.0-eof.diff
Created September 12, 2013 17:46
--- bwtdisk-0.9.0/bwtmerge.c.orig 2010-07-07 03:34:50.000000000 -0700
+++ bwtdisk-0.9.0/bwtmerge.c 2012-03-22 12:37:09.000000000 -0700
@@ -366,7 +366,11 @@
for(i=0;i<n;i++)
if(sa[i]==0) {
new_rank0=i; // rank of text[0..]
+#if 0
bwt[i+1] =bwt[i]; // to help compression
+#else
+ bwt[i+1] = 0;
@sjackman
sjackman / consensus_calling.h
Created September 19, 2013 19:54
// ==========================================================================
// consensus_calling.h
// ==========================================================================
// Copyright (c) 2006-2010, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
@sjackman
sjackman / wxmac.log
Created September 21, 2013 19:25
wxmac 2.9.5.0 Homebrew installation log
This file has been truncated, but you can view the full file.
==> Upgrading 1 outdated package, with result:
wxmac 2.9.5.0
==> Upgrading wxmac
rm /usr/local/bin/wxrc-2.9
rm /usr/local/bin/wxrc
rm /usr/local/bin/wx-config
rm /usr/local/include/wx-2.9
rm /usr/local/lib/wx
rm /usr/local/lib/python2.7/site-packages/wxPython-2.9.4.0-py2.7.egg-info
rm /usr/local/lib/python2.7/site-packages/wx/xrc.py
@sjackman
sjackman / wxmac.log
Created September 23, 2013 03:23
Homebrew build log of wxmac after installing both jpeg and libtiff with --universal
This file has been truncated, but you can view the full file.
==> Upgrading 1 outdated package, with result:
wxmac 2.9.5.0
==> Upgrading wxmac
rm /usr/local/bin/wxrc-2.9
rm /usr/local/bin/wxrc
rm /usr/local/bin/wx-config
rm /usr/local/include/wx-2.9
rm /usr/local/lib/wx
rm /usr/local/lib/python2.7/site-packages/wxPython-2.9.4.0-py2.7.egg-info
rm /usr/local/lib/python2.7/site-packages/wx/xrc.py
@sjackman
sjackman / BCL6-ST6GAL1.sam
Created September 26, 2013 18:57
BCL6 ST6GAL1 inversion
@SQ SN:chr3 LN:198022430
95 16 chr3 186698393 60 162M1D3974M37D2347M4I1440M1I4991M20D1374M2I555M1I15M2D3891M1D981M2D1558M1I1214M5I333M1D1557M1I209M2D2713M1D2580M1I9731M8I665M1I2930M1D540M2D55M6D489M4I1154M22043S * 0 0 AAAAAAAAAAAAAAAAAAAAATTAGCCAGGCAAGGTGGCAAGTGCCTGTAGTCCCAGCTATTAGGGAGGCTGAGGCAGGAAAATCACTTGAACCTGGGAGGTGGAGGTTGCAGTGAGGATCACCCCACTGCACACCAGCCTGGGTGACAGAGACTCCATCTCAAAAAAAAAAAAAAAAGATAGAAGTCAAGGGGAAATAGATTCTGGATCAATGAATCTATACTCTAATACTCTAAACTCAAAACTATCTGCAAGTGGGATGTGTGCCTTTATAGGTCCCTGTCACTAGTGGTCAAGCAATCAGTGCCATCACGTGTCGGGTGTGATGGCTGAGCTGTTCTTCAGGGACCCAGTCCTCAGTCAGTGTCTGCTGTATACATGCAGCTGCAGAGGACATTTGTGCACTGAGGAGGGCTTTGGGTGTGTTAATATTCTAGAAGAGGTGGAGTAGAGCAGCTATGCAAAGCAAGGAAGAAGGCAGGAGGTGTTAAAAGAAAAACTTTAGAGAAAATAAATGTAGCAAAGTTCATCTGAGCAAAGAACCATGTGTGAATTGGGCAGCACTCAGAACCAGAAGAGGTTCAGAGAGCTCTGCTGCCACAGTGAGGACAGTGAGCTTTTGTAGGCTGAACGTGGAAAGAAGACTAAGAAAATATATTTTATTAGAGTGGGAAGACCCTAGTTAGAGGTTAGTTGGTGGTTTCTGATTGGTGAAGCCTCTAGTTACATTTTACTGTTTACATTGATTTGGATTTTGGTTTGCTTATGTAGAAGCTCTGGTTATGGAGACAACCTCAGGCTAACGG
@sjackman
sjackman / joinx.log
Created September 26, 2013 20:48
Build log of joinx on OS X
==> Cloning https://github.com/genome/joinx.git
git --git-dir /Library/Caches/Homebrew/joinx--git/.git status -s
Updating /Library/Caches/Homebrew/joinx--git
git config remote.origin.url https://github.com/genome/joinx.git
git config remote.origin.fetch +refs/tags/v1.7.4:refs/tags/v1.7.4
git --git-dir /Library/Caches/Homebrew/joinx--git/.git rev-parse -q --verify v1.7.4
git checkout -f v1.7.4
HEAD is now at 350f063... update alternatives priority
git reset --hard v1.7.4
HEAD is now at 350f063 update alternatives priority
@sjackman
sjackman / pr374.log
Created October 8, 2013 17:11
git checkout pr/374 brew install -v trinity
==> Downloading http://downloads.sourceforge.net/trinityrnaseq/trinityrnaseq_r2013-02-25.tgz
Already downloaded: /Library/Caches/Homebrew/trinity-r2013-02-25.tgz
tar xf /Library/Caches/Homebrew/trinity-r2013-02-25.tgz
==> make
make
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
&& ./configure --prefix=`pwd` && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
@sjackman
sjackman / pr374-std-llvm.log
Created October 8, 2013 17:57
git checkout pr/374 brew install trinity --env=std --cc=llvm-gcc -v
==> Downloading http://downloads.sourceforge.net/trinityrnaseq/trinityrnaseq_r2013-02-25.tgz
Already downloaded: /Library/Caches/Homebrew/trinity-r2013-02-25.tgz
tar xf /Library/Caches/Homebrew/trinity-r2013-02-25.tgz
==> make
make
Using gnu compiler for Inchworm and Chrysalis
cd Inchworm && (test -e configure || autoreconf) \
&& ./configure --prefix=`pwd` && make install
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
@sjackman
sjackman / sam-to-coords.pl
Created October 16, 2013 23:03
Convert a SAM file to tab-delimited alignment coordinates
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use File::Spec;
my $script_name = (File::Spec->splitpath($0))[2];
@sjackman
sjackman / test-abyss-connectpairs.mk
Last active December 25, 2015 21:59
Test abyss-connectpairs
# Test abyss-connectpairs
# Parameters
j=2
k=20
g=100e3
# Phony targets
all: e0-connected.fa \