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remove duplicate unitigs (they are already deterministic) #816

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sebhtml opened this issue Nov 12, 2014 · 0 comments
Open

remove duplicate unitigs (they are already deterministic) #816

sebhtml opened this issue Nov 12, 2014 · 0 comments
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project=genomics
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sebhtml commented Nov 12, 2014

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@sebhtml sebhtml self-assigned this Dec 9, 2014
sebhtml pushed a commit to sebhtml/biosal that referenced this issue Jan 7, 2015
unitigs: remove duplicated paths
9b55133 
Before:

[boisvert@bigmem biosal]$ grep '>' output/unitigs.fasta |sort|uniq > signature1
[boisvert@bigmem biosal]$ sha1sum signature1
1b12ba2739e9cd1734304014d0cc11e6a1992a1f  signature1
[boisvert@bigmem biosal]$ ls -lh output/
total 7.2M
-rw-rw-r--. 1 boisvert boisvert 7.2M Jan  7 17:34 unitigs.fasta

After:

[boisvert@bigmem biosal]$ ls -lh output/
total 3.0M
-rw-rw-r--. 1 boisvert boisvert 3.0M Jan  7 17:40 unitigs.fasta
[boisvert@bigmem biosal]$ grep '>' output/unitigs.fasta |sort|uniq > signature1
[boisvert@bigmem biosal]$ sha1sum signature1
1b12ba2739e9cd1734304014d0cc11e6a1992a1f  signature1

There are still some duplications though.

Link: GeneAssembly/biosal#816
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
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