feat: refactor db subset CLI, add subset by VCF and subset by TxId op…

…tions (#641)

src/annotate/seqvars/provider.rs

@@ -97,6 +97,48 @@ impl TxIntervalTrees {
 
         (contig_to_idx, trees)
     }
+
+    pub fn get_tx_for_region(
+        &self,
+        tx_seq_db: &TxSeqDatabase,
+        alt_ac: &str,
+        _alt_aln_method: &str,
+        start_i: i32,
+        end_i: i32,
+    ) -> Result<Vec<TxForRegionRecord>, Error> {
+        let contig_idx = *self
+            .contig_to_idx
+            .get(alt_ac)
+            .ok_or(Error::NoTranscriptFound(alt_ac.to_string()))?;
+        let query = start_i..end_i;
+        let tx_idxs = self.trees[contig_idx].find(query);
+
+        Ok(tx_idxs
+            .iter()
+            .map(|entry| {
+                let tx = &tx_seq_db.tx_db.as_ref().expect("no tx_db?").transcripts
+                    [*entry.data() as usize];
+                assert_eq!(
+                    tx.genome_alignments.len(),
+                    1,
+                    "Can only have one alignment in Mehari"
+                );
+                let alt_strand = tx.genome_alignments.first().unwrap().strand;
+                TxForRegionRecord {
+                    tx_ac: tx.id.clone(),
+                    alt_ac: alt_ac.to_string(),
+                    alt_strand: match Strand::try_from(alt_strand).expect("invalid strand") {
+                        Strand::Plus => 1,
+                        Strand::Minus => -1,
+                        _ => unreachable!("invalid strand {}", alt_strand),
+                    },
+                    alt_aln_method: ALT_ALN_METHOD.to_string(),
+                    start_i,
+                    end_i,
+                }
+            })
+            .collect())
+    }
 }
 
 /// Configuration for constructing the `Provider`.