App-Sandy

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docker/README.md  view on Meta::CPAN

- `sandy_db` volume will be created at first run and will persist after container deletion.

```
$ docker run \
	--rm \
	-v sandy_db:/sandy/db
	galantelab/sandy
```

You can verify the created volume with the commands:

```
$ docker volume ls

# and in more detail with the command:
$ docker volume inspect sandy_db
```

#### Mounted directory:

- `/path/to/DB` will receive the default database at first run and any further changes will be stored in it.

```
$ docker run \
	--rm \
	-v /path/to/DB:/sandy/db \
	galantelab/sandy
```

Now, verify the directory `/path/to/DB`. You should find the file `db.sqlite3`.

As you add your custom patterns to **Sandy**, the alterations will be kept safelly outside the container.

#### More examples:

- Add a new quality profile:

```
$ docker run \
	--rm \

lib/App/Sandy/Simulator.pm  view on Meta::CPAN

			$piece_table{$seq_id} = $type_h;

		# else, just remove it!
		} else {
			push @blacklist => $seq_id;
		}
	}

	unless (%piece_table) {
		die "All fasta entries were removed due to deletions. ",
			"Please, verify the genomic variation '$genomic_variation'\n";
	}

	# If fasta_rtree has entries
	unless ($self->_has_no_fasta_rtree) {
		# Remove no valid entries from id -> pid relation
		$self->_delete_fasta_rtree(@blacklist) if @blacklist;
	}

	# Make the id -> pid relationship
	$self->_populate_fasta_tree;

lib/App/Sandy/Simulator.pm  view on Meta::CPAN

		for my $snv (@$snvs) {
			# Insertions may accur until one base after the
			# end of the sequence, not more
			if (($snv->{ref} eq '-' && $snv->{pos} > $size) || ($snv->{ref} ne '-' && $snv->{pos} >= $size)) {
				log_msg sprintf ":: In validating '%s': Position, %s/%s at %s:%d, outside fasta sequence",
					$genomic_variation, $snv->{ref}, $snv->{alt}, $seq_id, $snv->{pos} + 1;

				# Next snv
				next;
			# Deletions and changes. Just verify if the reference exists
			} elsif ($snv->{ref} ne '-') {
				my $ref = substr $$seq, $snv->{pos}, length($snv->{ref});

				if (uc($ref) ne uc($snv->{ref})) {
					log_msg sprintf ":: In validating '%s': Not found reference '%s' at fasta position %s:%d",
						$genomic_variation, $snv->{ref}, $seq_id, $snv->{pos} + 1;

					# Next snv
					next;
				}

ppport.h  view on Meta::CPAN

The default namespace is C<DPPP_>.

=back

The good thing is that most of the above can be checked by running
F<ppport.h> on your source code. See the next section for
details.

=head1 EXAMPLES

To verify whether F<ppport.h> is needed for your module, whether you
should make any changes to your code, and whether any special defines
should be used, F<ppport.h> can be run as a Perl script to check your
source code. Simply say:

    perl ppport.h

The result will usually be a list of patches suggesting changes
that should at least be acceptable, if not necessarily the most
efficient solution, or a fix for all possible problems.

ppport.h  view on Meta::CPAN

VTBL_substr|5.005003||Viu
VTBL_sv|5.005003||Viu
VTBL_taint|5.005003||Viu
VTBL_uvar|5.005003||Viu
VTBL_vec|5.005003||Viu
vTHX|5.006000||Viu
VT_NATIVE|5.021004||Viu
vtohl|5.003007||Viu
vtohs|5.003007||Viu
VUTIL_REPLACE_CORE|5.019008||Viu
vverify|5.009003|5.009003|
VVERIFY|5.019008||Viu
vwarn|5.006000|5.003007|
vwarner|5.006000|5.004000|p
wait4pid|5.003007||Viu
wait|5.005000||Viu
want_vtbl_bm|5.015000||Viu
want_vtbl_fm|5.015000||Viu
warn|5.003007||vV
WARN_ALL|5.006000|5.003007|p
WARN_ALLstring|5.006000||Viu