better locus at

src/lib.rs

@@ -7,7 +7,7 @@ use flate2::Compression;
 use serde::Serialize;
 use serde_json::{json, Value};
 use smart_default::SmartDefault;
-use std::{io::prelude::*, usize};
+use std::io::prelude::*;
 
 /// Compress string according to compressString from: https://github.com/igvteam/igv-utils/blob/master/src/bgzf.js#L125
 fn compress_string(input: &str) -> anyhow::Result<String> {
@@ -104,12 +104,20 @@ impl Session {
         Ok(self)
     }
 
-    pub fn with_locus_at(mut self, at: (String, i32)) -> anyhow::Result<Self> {
+    pub fn with_locus_at(
+        mut self,
+        (contig, position): (&str, u32),
+        plus_minus: u32,
+    ) -> anyhow::Result<Self> {
         *self
             .value
             .get_mut("locus")
-            .context("Can't access locus value")? =
-            json!(format!("{}:{}-{}", at.0, at.1 - 19, at.1 + 19));
+            .context("Can't access locus value")? = json!(format!(
+            "{}:{}-{}",
+            contig,
+            position.saturating_sub(plus_minus),
+            position + plus_minus
+        ));
         Ok(self)
     }
 
@@ -337,7 +345,7 @@ mod tests {
     fn it_works() -> anyhow::Result<()> {
         let sess = Session::default()
             .with_reference(ReferenceValues::default())
-            .with_locus_at(("chr1".to_string(), 47_098_189))?
+            .with_locus_at(("chr1", 47_098_189), 33)?
             .add_track(Track::Bam(BamTrack::new(
                 "ROBIN diag",
                 "/data/longreads_basic_pipe/ROBIN/diag/ROBIN_diag_hs1.bam",
@@ -352,8 +360,35 @@ mod tests {
             )))?
             .add_track(Track::Genes(GenesTrack::new(
                 "/data/ref/hs1/chm13v2.0_RefSeq_Liftoff_v5.1_sorted.gff3.gz",
-            )))?
-        ;
+            )))?;
+        let compressed_str = sess.link("http://store-desktop.local/igv/")?;
+        println!("{compressed_str}");
+        Ok(())
+    }
+
+    #[test]
+    fn denovo_link() -> anyhow::Result<()> {
+        let id = "ACHITE";
+        let chr = "chr1";
+        let alt_id = "47108362-81682505_8090_wtdbg2";
+        let alt_prefix = format!("/data/longreads_basic_pipe/{id}/diag/assemblies/{chr}/{alt_id}");
+
+        let reference = ReferenceValues {
+            id: "contig".to_string(),
+            name: "de novo".to_owned(),
+            fasta_url: format!("{alt_prefix}.fa"),
+            index_url: format!("{alt_prefix}.fa.fai"),
+            cytoband_url: "".to_string(),
+            alias_url: "".to_owned(),
+        };
+
+        let sess = Session::default()
+            .with_reference(reference)
+            .with_locus_at((alt_id, 100), 19)?
+            .add_track(Track::Bam(BamTrack::new(
+                "On contig",
+                &format!("{alt_prefix}.bam"),
+            )))?;
         let compressed_str = sess.link("http://store-desktop.local/igv/")?;
         println!("{compressed_str}");
         Ok(())