[Bioperl-l] unaligned sequences breaks hqd analysis

[Robson Francisco de Souza]

	Hi Andy,

On Wed, 5 Mar 2003, Andy Nunberg wrote:
> I am glad you survived Carnival :)

	I wouldn't say that I survived... :-)
<snip>
> so i looked at each sequence as it was looping,
> turns out that the sequence it was breaking on has -1 -1 as the align start
> and stop
> Ideally, one would check to see which seqs in the contig are aligned before
> calling the coordinates of the aligned section
> I have inserted
> next if !$coord and that seems to work as short term fix

	Right, I did notice this problem in one of my tests. I'll add your
fix soon. Thanks.
				Robson

> Andy
> *******************************************************************
> Andy Nunberg, Ph.D
> Computational Biologist
> Orion Genomics, LLC 
> (314) 615-6989
> http://www.oriongenomics.com
> 
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