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bigdatagenomics / bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
Apache License 2.0
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Fix avro-maven-plugin version 1.11.1 warnings #214

Closed heuermh closed 1 year ago

heuermh commented 1 year ago 
$ mvn install
...
[INFO] --- avro-maven-plugin:1.11.1:idl-protocol (schemas) @ bdg-formats ---
[WARNING] Found documentation comment at line 493, column 3. Ignoring previous one at line 486, column 3: "Chromosome does not exist in reference genome database. Typically indicates
a mismatch between the chromosome names in the input file and the chromosome
names used in the reference genome. Message code E1."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 499, column 3. Ignoring previous one at line 493, column 3: "The variant's genomic coordinate is greater than chromosome's length.
Message code E2."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 507, column 3. Ignoring previous one at line 499, column 3: "The 'REF' field in the input VCF file does not match the reference genome.
This warning may indicate a conflict between input data and data from
reference genome (for instance is the input VCF was aligned to a different
reference genome). Message code W1."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 513, column 3. Ignoring previous one at line 507, column 3: "Reference sequence is not available, thus no inference could be performed.
Message code W2."
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[WARNING] Found documentation comment at line 520, column 3. Ignoring previous one at line 513, column 3: "A protein coding transcript having a nonmultiple of 3 length. It indicates
that the reference genome has missing information about this particular
transcript. Message code W3."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 527, column 3. Ignoring previous one at line 520, column 3: "A protein coding transcript has two or more STOP codons in the middle of
the coding sequence (CDS). This should not happen and it usually means the
reference genome may have an error in this transcript. Message code W4."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 535, column 3. Ignoring previous one at line 527, column 3: "A protein coding transcript does not have a proper START codon. It is
rare that a real transcript does not have a START codon, so this probably
indicates an error or missing information in the reference genome.
Message code W5."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 542, column 3. Ignoring previous one at line 535, column 3: "Variant has been realigned to the most 3prime position within the
transcript. This is usually done to to comply with HGVS specification
to always report the most 3prime annotation. Message code I1."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 549, column 3. Ignoring previous one at line 542, column 3: "This effect is a result of combining more than one variants (e.g. two
consecutive SNPs that conform an MNP, or two consecutive frame_shift
variants that compensate frame). Message code I2."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Ignoring out-of-place documentation comment at line 549, column 3: "An alternative reference sequence was used to calculate this annotation
(e.g. cancer sample comparing somatic vs. germline). Message code I3."
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[WARNING] Found documentation comment at line 566, column 3. Ignoring previous one at line 561, column 3: "High impact."
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[WARNING] Found documentation comment at line 571, column 3. Ignoring previous one at line 566, column 3: "Moderate impact."
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[WARNING] Found documentation comment at line 576, column 3. Ignoring previous one at line 571, column 3: "Low impact."
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[WARNING] Ignoring out-of-place documentation comment at line 576, column 3: "Modifier impact."
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[WARNING] Found documentation comment at line 592, column 3. Ignoring previous one at line 587, column 3: "Forward ("+") strand."
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[WARNING] Found documentation comment at line 597, column 3. Ignoring previous one at line 592, column 3: "Reverse ("-") strand."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 602, column 3. Ignoring previous one at line 597, column 3: "Independent or not stranded (".")."
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[WARNING] Ignoring out-of-place documentation comment at line 602, column 3: "Strandedness is relevant, but unknown ("?")."
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[WARNING] Found documentation comment at line 970, column 3. Ignoring previous one at line 965, column 3: "The genotype is the reference allele."
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[WARNING] Found documentation comment at line 975, column 3. Ignoring previous one at line 970, column 3: "The genotype is the alternate allele."
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[WARNING] Found documentation comment at line 981, column 3. Ignoring previous one at line 975, column 3: "The genotype is an unspecified other alternate allele. This occurs in our schema
when we have split a multi-allelic genotype into two genotype records."
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[WARNING] Ignoring out-of-place documentation comment at line 981, column 3: "The genotype could not be called."
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[WARNING] Found documentation comment at line 997, column 3. Ignoring previous one at line 992, column 3: "All genotypes at this site were called as the reference allele."
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[WARNING] Found documentation comment at line 1005, column 3. Ignoring previous one at line 997, column 3: "Genotypes at this site were called as multiple different alleles. This
most commonly occurs if a diploid sample's genotype contains one reference
and one variant allele, but can also occur if the genotype contains multiple
alternate alleles."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 1010, column 3. Ignoring previous one at line 1005, column 3: "All genotypes at this site were called as a single alternate allele."
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[WARNING] Ignoring out-of-place documentation comment at line 1010, column 3: "The genotype could not be called at this site."
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[WARNING] Found documentation comment at line 1491, column 3. Ignoring previous one at line 1486, column 3: "DNA alphabet."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Found documentation comment at line 1496, column 3. Ignoring previous one at line 1491, column 3: "RNA alphabet."
Did you mean to use a multiline comment ( /* ... */ ) instead?
[WARNING] Ignoring out-of-place documentation comment at line 1496, column 3: "Protein alphabet."
Did you mean to use a multiline comment ( /* ... */ ) instead?
heuermh commented 1 year ago

Closing as WontFix, these enum value doc fields were not supported before.