added sam functionality, updated README, Write to SAM/BAM - #1

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mjsull wants to merge 30 commits into

BeatsonLab-MicrobialGenomics:masterfrom

Commits on Feb 25, 2015

Merge pull request #1 from BeatsonLab-MicrobialGenomics/master
mjsull
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8adaf29

Commits on Mar 9, 2015

Something weird happened on merge, readded current? version of DiscoPlot
mjsull
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55568c2

Commits on Mar 10, 2015

fixed to contain current version of DiscoPlot
mjsull
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a9cde26
fixed to contain current version of DiscoPlot
mjsull
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6502306

Commits on Apr 30, 2015

started coding sam functionality
mjsull
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72b9559
sam functionality finished
mjsull
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5aa677a
removed text finsihed readsm
mjsull
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28e89f8

Commits on May 1, 2015

sam functionality complete
mjsull
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858c70c
don't require pysam for windows installation
mjsull
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0bec601
typo
mjsull
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8012bd1

Commits on May 2, 2015

updated README
mjsull
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2680dcf
fixed image link
mjsull
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878d589
fixing README
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cd1f1f5
testing
mjsull
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fe9d145
fixed README
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5690035
fixed quickstart
mjsull
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bbf4f93
fixed
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879bf9d
fixed?
mjsull
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ab0c8a6
fixed?
mjsull
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3137ce9
fixed typo in help
mjsull
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81ea51d
small fix
mjsull
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8afd796

Commits on May 4, 2015

Update setup.py
mjsull
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d09f703

Commits on Jun 3, 2015

Update README.rst
mjsull
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14893ba

Commits on Jul 11, 2015

updated version number, fixed CITATION
mjsull
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0d05f72
updated requirements
mjsull
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13c702f
incremented version
mjsull
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10cd3e4

Commits on Aug 27, 2015

Cleaned up files for release with cxFreeze
mjsull
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116538f

Commits on Aug 28, 2015

changed setup.py to for use with cx_Freeze
mjsull
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21bd9e4
updated requirements
mjsull
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a069c22

Commits on Sep 2, 2015

clean up
mjsull
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34d407f