fix: ensure trailing newline is included when parsing GFF3 region #1573
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Resolves #1572 When parsing GFF3, we split up the file on `#sequence-region` pragma blocks. As per specification, there could be multiple of them, and we want to know about this. The `bio` crate's `GffReader` does not support regions, so we do the splitting manually and then pass each region's slice to `bio` `GffReader`. However, due to mistakenly trimmed trailing newlines in the regions on our side, `bio` GFF3 parser would fail when it encounters a commented line as a last line of the region. The error and repro is described in #1572. In this PR I: - [x] make sure that the region content string is properly extracted, including the trailing newline character - [x] remove `.trim()` call such that this newline isn't removed This way `bio` can understand our GFF3 blocks even when they have comments.
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Resolves #1572
When parsing GFF3, we split up the file on
#sequence-regionpragma blocks. As per specification, there could be multiple of them, and we want to know about this.The
biocrate'sGffReaderdoes not support regions, so we do the splitting manually and then pass each region's slice tobioGffReader. However, due to mistakenly trimmed trailing newlines in the regions on our side,bioGFF3 parser would fail when it encounters a commented line as a last line of the region. The error and repro is described in #1572.In this PR I:
.trim()call such that this newline isn't removedThis way
biocan understand our GFF3 blocks even when they have comments.