Vcf gz datatype #4254
Vcf gz datatype #4254
Conversation
|
@galaxybot test this |
mvdbeek
added
area/datatypes
kind/feature
status/review
and removed
status/WIP
triage
labels
lib/galaxy/datatypes/tabular.py
Outdated
| f.seek(offset) | ||
| ck_data = f.read(ck_size or trans.app.config.display_chunk_size) | ||
| if ck_data and ck_data[-1] != '\n': | ||
| f = compression_utils.get_fileobj(dataset.file_name) |
There was a problem hiding this comment.
I think we can do with compression_utils.get_fileobj(dataset.file_name) as f:.
|
@ffinfo let me know if you want to continue working on this (I think we're almost there), otherwise I can do the last bit of polishing. |
|
@mvdbeek Ye was still planning to continue on this. I think I still have some uncommitted code for a test tool. Was a bit of a chaos when I did came back to Leiden. You know how that goes with todo's ;) |
test/functional/tools/vcf_bgzip.xml
Outdated
| <param name="input" format="vcf_bgzip" type="data" label="Source file"/> | ||
| </inputs> | ||
| <outputs> | ||
| <data format="data" ftype="vcf_bgzip" name="output" /> |
There was a problem hiding this comment.
This should be format="vcf_bgzip". ftype is (confusingly ...) only used in the test section.
|
@galaxybot test this |
This adds support for uploading VcfGz files in the upload box. When a user does this, the file will not be uncompressed. Also adds uncompressed preview. TODO: - Move Vcf class to BaseVcf - Vcf and VcfGz should both inherit from BaseVcf - Add a metadata element for VcfGz indexes (vzf.gz.tbi) - Create index (in set_meta method of VcfGz class) - Write test tools This is a kcikstart to @ffinfo GCC hack project.
…_datatypes_conf.xml
|
@galaxybot test this |
|
@ffinfo this is looking good to me, If you're happy with this I can merge it. bctools generates csi indexes by default (i.e without the |
|
Well tools like Picard and GATK are using by default '.tbi' extensions. The csi is more used for bcf files and not for vcf files. That why I think it's better to keep it with the '-t' flag |
|
Alright, we can always add this if there is demand. |
mvdbeek
force-pushed
the
vcf_gz_datatype
branch
from
13d32ee to
05e9cab
Compare
|
@galaxybot test this |
mvdbeek
force-pushed
the
vcf_gz_datatype
branch
from
05e9cab to
ed67b11
Compare
|
@galaxybot test this |
In galaxyproject#4254 `vcf_bgzip` was made a proper datatype with the introduction of the `VcfGz` class, but was still described as a subclass in `datatypes_conf.xml` . Also fix `file_ext` attribute in `BaseVcf` and subclasses.
No description provided.