works with sequences sharing same ids

[FredericBGA]

a need that pop-up today from one of my colleague.

[peterjc]

Just looking at the code I don't understand the goal here - do you have a simplified example with the before/after behaviour?

[FredericBGA]

Of course.

I had updated the tests accordingly.

before this PR, with this kind of file:

>7
ATGC
>7
ATGC

the result:

>7;7 representing 2 records
ATGC
>7;7 representing 2 records
ATGC

now the result file is:

>7;7 representing 2 records
ATGC

We often have this case, as we fetch sequences from various sources or people and try to merge them.

Is this clear for you?

[FredericBGA]

The failed tests are not related to this PR, right?

[peterjc]

This is input query files with repeated identifiers?

Repeated entries with the same identifier and sequence are one thing, repeated identifiers with different sequence are another. Personally I would make these an error condition - they cause too many problems downstream.

[peterjc]

The tool's master branch is failing on TravisCI against the Galaxy dev branch, see #120

[FredericBGA]

you're right, the output is not yet perfect in this case:

>1
A
>1
A
>1
T

the output was:

>1;1 representing 2 records
A
>1;1 representing 2 records
A
>1;1 representing 2 records
T

with this PR it's now (and not good either...):

>1;1 representing 2 records
A

[FredericBGA]

@peterjc This new version works for what I was needed. I let you review the code and merge if you want. Thank you for your comments.