upgrade spades for nicer error messages

[SherineAwad]

• [x] the changes show correct formatting when built with Sphinx;
• [ ] the changes have been reviewed by someone other than the original author;
• [x] the changes work under our literate-resting tests with a small data set;

[SherineAwad]

@ctb: Please don't merge. Work in progress

[SherineAwad]

@ctb idba assembler sometimes doesn't generate scaffolds (happens with Podar set without inflation), so I have to update calc-best-assembly command to capture contig.fa instead of scaffold.fa. Should I update it in the protocol just in case no scaffolds are generated?

[ctb]

Let's put this on the list of things to talk about. Can you add this as a separate issue in khmer-protocols? Also, does it crash, or what? What happens? Is this a memory problem?

[SherineAwad]

@ctb ..ping. Or ping discussion about it. Either to remove scaffolds and replace it by contig.fa?

[ctb]

On Sun, Jul 20, 2014 at 03:06:36PM -0700, Sherine Mahmoud wrote:

@ctb ..ping. Or ping discussion about it. Either to remove scaffolds and replace it by contig.fa?

scaffols are probably better if they exist. But I think what we really need to do is alert people when assemblers fail...

C. Titus Brown, ctb@msu.edu

[SherineAwad]

@ctb Please take a look and I am fine with merge.

[qingpeng]

Is there any explanation about the failure to generate scaffolds in idba documentation? If it is normal that no scaffolds are generated by idba sometimes, I think it is reasonable to at least make a note about this.

On Jul 21, 2014, at 6:06 AM, Sherine Mahmoud notifications@github.com wrote:

@ctb ..ping. Or ping discussion about it. Either to remove scaffolds and replace it by contig.fa?

— Reply to this email directly or view it on GitHub.

[ctb]

Merged!