openvax / isovar
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LAST BUILD ON BRANCH cli/input-errors
branch: cli/input-errors
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coverage: 95.516% (+0.009%) from 95.507%
35041952767

Pull #260

github

iskandr 
Merge master, set version to 1.11.2, stop rejecting legal inputs

master moved to 1.11.0 (#263) after this branch was cut, so 1.10.4 would
have been a downgrade; 1.11.2 leaves 1.11.1 for #259.

Review fixes to the new validation, each of which rejected input that
works on master:

- Remote paths. isfile() is False for any URL, but htslib opens
  http/https/s3/gs BAMs directly and varcode's load_vcf downloads HTTP(S)
  VCFs to a temp file. Skip the existence check and the AlignmentFile
  probe (which would force a network round trip at parse time) when the
  path carries a URL scheme. The scheme regex requires two or more
  characters before "://" so a Windows drive letter isn't mistaken for one.

- --output with a leading "~". pandas expands it when writing, so expand
  it here too before asking whether the directory exists.

- --genome alongside --maf only. varcode ignores --genome for MAF files
  since each row names its own reference, so only validate it when --vcf
  or --variant will actually consume it.

Also move the has_index check into an else: on the try, so it can't read
an unbound name, and drop the redundant local pytest import and the
positional args_with_bam[-1] lookup in the tests.

Claude-Session: https://claude.ai/code/session_01DctgBZ5rJiuNzpWXqrNguT
Pull Request #260: Check CLI inputs before loading reads

50 of 52 new or added lines in 10 files covered. (96.15%)

3110 of 3256 relevant lines covered (95.52%)

0.96 hits per line

Relevant lines Covered
3256 RELEVANT LINES 3110 COVERED LINES
0.96 HITS PER LINE
Source Files on cli/input-errors

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
35041952767 cli/input-errors Merge master, set version to 1.11.2, stop rejecting legal inputs master moved to 1.11.0 (#263) after this branch was cut, so 1.10.4 would have been a downgrade; 1.11.2 leaves 1.11.1 for #259. Review fixes to the new validation, each of which rej... Pull #260 iskandr github
95.52
35009320795 cli/input-errors Check CLI inputs before loading reads All eight commands now check parsed arguments up front and exit with an argparse error (status 2) instead of a traceback when: - a --vcf, --maf, --json-variants or --bam file is missing - --bam is not an inde... Pull #260 iskandr github
95.48
35009359460 cli/input-errors Merge 6cd41b883 into 408f5e01c Pull #260 web-flow github
95.48
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