Does Staden io_lib support reading FASTQ content into a Read object? If not, can you point me to where in the code I would begin to add such support myself? It appears there are multiple "standards" for encoding the quality data and it would be nice if I could use a library like io_lib to handle handle that nonsense for me. :-) I see there is a program to convert scf to fastq, but didn't see anything for the other way around.
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On Mon, May 23, 2016 at 01:12:39PM +0000, Will Stokes wrote:
Does Staden io_lib support reading FASTQ content into a Read object?
No, sorry. It's probably be a bit of a heavy-weight API for fastq
too.
If not, can you point me to where in the code I would begin to add
such support myself? It appears there are multiple "standards" for
encoding the quality data and it would be nice if I could use a
library like io_lib to handle handle that nonsense for me. :-) I see
there is a program to convert scf to fastq, but didn't see anything
for the other way around.
The only code in the Staden Package that deals with fastq would be in
Gap5 itself (in the confusingly named staden/src/gap5/fasta.c).
Possibly that should have been added to io_lib, but for whatever
reason at the time I didn't (I can't think why - probably just
laziness).
However it doesn't deal with the multiple ways of encoding quality.
Frankly I'd be inclined to ignore all other fastq anyway except the
standard qval + 33 ('!'). The others were invented by Illumina (and
subsequently dropped again I believe).
Processing fastq yourself though isn't hard provided you make sure to
use the length of the sequence as the indicator for how many quality
values you should expect. Ie don't fall into the pit fall of a line
of qualities starting with "@" represents the next sequence identifier
if we haven't yet read enough quality values. Other than that it's
such a simple format you can just roll your own with relatively few
lines.
James
--
James Bonfield (jkb@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
On Mon, May 23, 2016 at 01:12:39PM +0000, Will Stokes wrote:
Does Staden io_lib support reading FASTQ content into a Read object?
No, sorry. It's probably be a bit of a heavy-weight API for fastq
too.
If not, can you point me to where in the code I would begin to add
such support myself? It appears there are multiple "standards" for
encoding the quality data and it would be nice if I could use a
library like io_lib to handle handle that nonsense for me. :-) I see
there is a program to convert scf to fastq, but didn't see anything
for the other way around.
The only code in the Staden Package that deals with fastq would be in
Gap5 itself (in the confusingly named staden/src/gap5/fasta.c).
Possibly that should have been added to io_lib, but for whatever
reason at the time I didn't (I can't think why - probably just
laziness).
However it doesn't deal with the multiple ways of encoding quality.
Frankly I'd be inclined to ignore all other fastq anyway except the
standard qval + 33 ('!'). The others were invented by Illumina (and
subsequently dropped again I believe).
Processing fastq yourself though isn't hard provided you make sure to
use the length of the sequence as the indicator for how many quality
values you should expect. Ie don't fall into the pit fall of a line
of qualities starting with "@" represents the next sequence identifier
if we haven't yet read enough quality values. Other than that it's
such a simple format you can just roll your own with relatively few
lines.
James
--
James Bonfield (jkb@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia
Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
Does Staden io_lib support reading FASTQ content into a Read object? If not, can you point me to where in the code I would begin to add such support myself? It appears there are multiple "standards" for encoding the quality data and it would be nice if I could use a library like io_lib to handle handle that nonsense for me. :-) I see there is a program to convert scf to fastq, but didn't see anything for the other way around.
On Mon, May 23, 2016 at 01:12:39PM +0000, Will Stokes wrote:
No, sorry. It's probably be a bit of a heavy-weight API for fastq
too.
The only code in the Staden Package that deals with fastq would be in
Gap5 itself (in the confusingly named staden/src/gap5/fasta.c).
Possibly that should have been added to io_lib, but for whatever
reason at the time I didn't (I can't think why - probably just
laziness).
However it doesn't deal with the multiple ways of encoding quality.
Frankly I'd be inclined to ignore all other fastq anyway except the
standard qval + 33 ('!'). The others were invented by Illumina (and
subsequently dropped again I believe).
Processing fastq yourself though isn't hard provided you make sure to
use the length of the sequence as the indicator for how many quality
values you should expect. Ie don't fall into the pit fall of a line
of qualities starting with "@" represents the next sequence identifier
if we haven't yet read enough quality values. Other than that it's
such a simple format you can just roll your own with relatively few
lines.
James
--
James Bonfield (jkb@sanger.ac.uk) | Hora aderat briligi. Nunc et Slythia Tova
| Plurima gyrabant gymbolitare vabo;
A Staden Package developer: | Et Borogovorum mimzebant undique formae,
https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi.
--
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.
Thanks, I appreciate the quick reply and suggestion.
Will Stokes
Chief Software Architect
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On Mon, May 23, 2016 at 12:27 PM, James Bonfield jkbonfield@users.sf.net
wrote: