GitLab

istream initializes the buffer buf while gzstreambase constructor opens the file and
may set some flags (in case the file can't be opened). If istream is called last
it will overwrite the flags that have been set

Now Vidjil may load .gz files.

Even if the CGI fails for an unknown reason we still have the content type, which should
satisty the web server

I thought mkstemp would do that by itself. While it may seem not very satistfactory to hardcode
the path, /tmp is POSIX.

See 183ad875.

This code was duplicated in 60a8bf4a.

This test was already working, but threw an exception, and the test coverage could be ignored.

Simplification of the code.

Closes bug tested by 14b16e9c.

Bug: With a reasonnably large -r option (such as 2000), no representative is found.
This is because min_cover is larger than max_auditioned.

If -w is below the seed weight (hence the junction size), strange things may happen,
as for example a clone without representative.

Closes bug created by 59a1bcf6.

59a1bcf6 added some spurious output that breaks CGI.
Thanks to @mikael-s for pointing that out.

Kmer is used inside a IKmerStore<Kmer>, its constructor should thus accept
the (label, stand) parameters.

We had too few gcc warnings.

When exception is thrown from constructor, the destructor is not called

operator<< for Sequence already outputs one. No need to add another one

When the Sequence contains quality information, it outputs a FASTQ rather than a FASTA.
This may be useful is one day we output FASTQ information (we never know, isn't it?)