search

bingxiao / biopieces

Automatically exported from code.google.com/p/biopieces
0 stars 0 forks source link

assemble_tag_contigs doesn't work #16

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. reading a bed file with 0 for all score values
2.
3.

What is the expected output? What do you see instead?
contigs, nothing. empty output

What version of the product are you using? On what operating system?

Please provide any additional information below.

Original issue reported on code.google.com by martinal...@gmail.com on 20 Feb 2009 at 6:19

GoogleCodeExporter commented 9 years ago 
Thanks Martin, I will have a look at it as soon as I get a computer! It may 
take a
couple of weeks. The bug is probably a typical Perl issue where I have used a 
"if
$score" where the correct should have been "if defined $score". That is a lame 
Perl
thing that gets me often.

Original comment by martinah...@gmail.com on 2 Mar 2009 at 3:39

GoogleCodeExporter commented 9 years ago 
assemble_tag_contigs work as expected. SCORE values of 0 indicates that these 
entries
are below threshold, and therefore no tag contigs are output: 

"Thus, tags are only assembled into tag contigs if their expression level is
higher than their repetitiveness; a tag sequenced 10 times, i.e. with a clone
count of 10, will only be considered if was found in the genome fewer than 10
times, i.e. have a SCORE below 10."

Original comment by martinah...@gmail.com on 25 Jul 2009 at 8:16