prolific, DynamicProgramming.hpp, argument incompatibility

[tedholzman]

in the DynamicProgramming.hpp file, on line 8087 there is a min() function call. The arguments are of different types that C++ finds incompatible. Changing the line to read:

m_sequence_count = ( ( sequence_count == 0 ) ? sequences->size() : min( (size_t) sequence_count, sequences->size() ) );

i.e. adding (size_t) cast, repairs it.

[pedlefsen]

Hi Ted. I wonder if replying to this will work? My vague belief is
that casts in c++ should preferably be like:
static_cast(value)..
Paul

On Fri, Nov 4, 2011 at 5:14 PM, Ted Holzman
[email protected]
wrote:

in the DynamicProgramming.hpp file, on line 8087 there is a min() function call.  The arguments are of different types that C++ finds incompatible.  Changing the line to read:

m_sequence_count = ( ( sequence_count == 0 ) ? sequences->size() : min( (size_t) sequence_count, sequences->size() ) );

i.e. adding (size_t)  cast, repairs it.

---

Reply to this email directly or view it on GitHub:
#7

[tedholzman]

On 11/4/11 5:25 PM, Paul T. Edlefsen wrote:

Hi Ted. I wonder if replying to this will work? My vague belief is
that casts in c++ should preferably be like:
static_cast(value)..
Paul

On Fri, Nov 4, 2011 at 5:14 PM, Ted Holzman
[email protected]
wrote:

in the DynamicProgramming.hpp file, on line 8087 there is a min() function call. The arguments are of different types that C++ finds incompatible. Changing the line to read:

m_sequence_count = ( ( sequence_count == 0 ) ? sequences->size() : min( (size_t) sequence_count, sequences->size() ) );

i.e. adding (size_t) cast, repairs it.

---

Reply to this email directly or view it on GitHub:
#7

---

Reply to this email directly or view it on GitHub:
#7 (comment)
Yes. I think that ought to work. I think the incompatibility is in
the "const" storage of one versus the stack storage of the other.

               -Ted

[pedlefsen]

---------- Forwarded message ----------
From: Diem, Kurt [email protected]
Date: Mon, Aug 13, 2012 at 3:43 PM
Subject: different herpes project
To: "Paul T. Edlefsen" [email protected]

**

Paul,

I know you are busy but there is another herpes project Larry would like
you to consider. Surprisingly, at this time the number of circulating
strains of HSV2 in the US is poorly understood and more investigation could
impact vaccine design. The AiCuris company has been testing a new drug for
herpes treatment. We have been doing traditional sequencing to check for
drug resistance in two genes, UL5 and UL52. I have made simple neighbor
joining trees and to my eyes there may be more than one strain present but
I believe you have more phylogenetic tools and skills than I do. From this
data can we say anything about the minimum number of clades circulating in
the US and is there evidence of recombination among clades? See attached
for NJ tree files(actually UL5 is a ML tree). If you would like the
sequences themselves or more information, let me know.

Kurt
206-667-3117