Graceful error on gff3.gz files #4489
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Instead of failing to parse a bgzipped annotation file, just error early with an explanation.
adamnovak
approved these changes
Jan 7, 2025
adamnovak
reviewed
Jan 7, 2025
src/subcommand/rna_main.cpp
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| @@ -92,6 +92,7 @@ int32_t main_rna(int32_t argc, char** argv) { | |||
| string hap_gbwt_out_filename = ""; | |||
| int32_t num_threads = 1; | |||
| bool show_progress = false; | |||
| string gz_suffix = ".gz"; | |||
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This might want to be GZ_SUFFIX and placed not right next to all the CLI parameters. Otherwise I expect there to be a CLI option to change it.
Co-authored-by: Adam Novak <anovak@soe.ucsc.edu>
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Changelog Entry
To be copied to the draft changelog by merger:
vg rnacan't parse.gzfiles, have it give a useful error for those inputs (resolve vg rna can't parse bgzipped GFF3 #4459)Description
Currently,
.gzfiles will be accepted forvg rna's--transcriptsor--intronsflags, but when we actually try to parse them it fails. This change auto-detects such files via the.gzextension and gives a useful error message. This will have false positives and false negatives, since it relies on the filenames following convention, but actually reading the file and detecting compression is much more difficult.