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Almost works
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Chiara Rasi committed Oct 18, 2024
1 parent 476c2ef commit b935beb
Showing 4 changed files with 18 additions and 2 deletions.
4 changes: 4 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -2,6 +2,10 @@
### Fixed
- Addressed the `Starlette Denial of service (DoS) via multipart/form-data` by updating starlette library. among others

## [unreleased]
### Added
- Refseq transcripts names on coverage overview page

## [2.0]
### Added
- Improve report explanation to better interpret average coverage and coverage completeness stats shown on the coverage report
5 changes: 5 additions & 0 deletions src/chanjo2/meta/handle_d4.py
Original file line number Diff line number Diff line change
@@ -86,6 +86,11 @@ def get_report_sample_interval_coverage(
interval_hgnc_symbol,
interval_hgnc_id,
interval.ensembl_id,
{
"mane_select": interval.refseq_mane_select,
"mane_plus_clinical": interval.refseq_mane_plus_clinical,
"mrna": interval.refseq_mane_select,
},
sample_name,
round(interval_coverage_at_threshold * 100, 2),
)
7 changes: 6 additions & 1 deletion src/chanjo2/meta/handle_report_contents.py
Original file line number Diff line number Diff line change
@@ -133,7 +133,12 @@ def get_report_data(
db=session,
interval_type=INTERVAL_TYPE_SQL_TYPE[query.interval_type],
genes=genes,
transcript_tags=[TranscriptTag.REFSEQ_MRNA],
transcript_tags=[
TranscriptTag.REFSEQ_MRNA,
TranscriptTag.REFSEQ_MANE_PLUS_CLINICAL,
TranscriptTag.REFSEQ_MANE_SELECT,
TranscriptTag.REFSEQ_MRNA,
],
)

for sample in query.samples:
4 changes: 3 additions & 1 deletion src/chanjo2/templates/overview.html
Original file line number Diff line number Diff line change
@@ -39,6 +39,7 @@
<tr>
<th scope="col">Gene</th>
<th scope="col">{{ extras.interval_type }}</th>
<th></th>
<th scope="col">Sample</th>
<th scope="col">Completeness {{ extras.default_level }}x [%]</th>
</tr>
@@ -52,7 +53,8 @@
</a>
</td>
<td>{{ row[2] }}</td>
<td>{{ row[3] }}</td>
<td>{{ row }}</td>
<td>{{ row[4] }}</td>
<td class="text-right">{{ row[4] }}</td>
</tr>
{% else %}

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