Change files names and reads names (modified)

[florealcab]

We usually use fastq files names as name of samples. So user must specify it, without any suffix. Also we add this name as a read name prefix, so read names are uniq, also between several samples.

(add missing updates from precedent pull request)

[galaxy001]

Would you please use tab for indent instead of 4 spaces ?

Reading a diff changing every line is quite a burden.

[florealcab]

I just commit with raplacing spaces with tabes.

[galaxy001]

Output dir may not exists, and pirs fails to create output file without the dir. Please add checking and make the dir.

Dumping simulation parameters in read name is useful, thus please restore them as:

--- a/src/pirs/pirs_simulate.cpp
+++ b/src/pirs/pirs_simulate.cpp
@@ -677,9 +677,10 @@ SimulationProfiles::~SimulationProfiles()
  */
 static void output_read(const Read &read, OutputStream &out_file)
 {
-       out_file.printf("%c%s_read_%"PRIu64"/%d\n",
+       out_file.printf("%c%s_read_%d_%"PRIu64"/%d\n",
                                        (read.quality_vals.empty()) ? '>' : '@',
-                                       read.indiv_name.c_str(), read.pair.pair_number, read.num_in_pair());
+                                       read.indiv_name.c_str(), read.pair.insert_len_mean,
+                                       read.pair.pair_number, read.num_in_pair());
        out_file.write(&read.seq[0], read.seq.size());
        out_file.putc('\n');

[florealcab]

Now output directory is checked and created is not exists (using boost library, to be cross-platform). We need to don't dump infos, so I restore like you said and I add an option to don't dump (not enabled by default)

[galaxy001]

I find stat is already in POSIX_C_SOURCE>=200112L, thus we do not need the heavy boost. At least both Linux and Mac have manpage for it. See https://stackoverflow.com/a/9314702/159695 or https://www.quora.com/How-do-I-check-if-a-directory-exists-in-Linux-using-C%2B%2B/answer/Syd-Logan?srid=uBEo.

On dumping info., I think we can make indiv-name optional to act as the switch. If indiv-name is supplied, no dumping as your ways before, if not supplied, the default value for indiv-name is Sim_%read_len_%insert_len_mean.

[florealcab]

As you asked, I now remove boost dependency, using stat instead. I also use now indiv_name parameter as a switch. Tell me if there is still a problem.