Quick script to pull down HLA-A from a test BAM file

go.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+set -euxo pipefail
+
+cargo build --release >/dev/null 2>&1
+
+./target/debug/hidive fetch \
+	-r \
+	-o HG002.HLA-A.bam \
+	-l chr6:29,940,532-29,947,870 \
+	gs://fc-bb12940d-f7ba-4515-8a98-42de84f63c34/HPRC_grch38/PBCCSWholeGenome/HG002/alignments/HG002.bam
+
+samtools index HG002.HLA-A.bam 

src/skydive/src/stage.rs

@@ -225,7 +225,7 @@ pub fn stage_data(
             reads
                 .iter()
                 .for_each(|read| {
-                    if !seen_read_ids.contains(read.qname()) && read_spans_locus(read.reference_start(), read.reference_end(), loci) {
+                    if !seen_read_ids.contains(read.qname()) && (!require_spanning_reads || read_spans_locus(read.reference_start(), read.reference_end(), loci)) {
                         let _ = bam_writer.write(read);
                     }
 

src/skydive/src/utils.rs

@@ -29,28 +29,29 @@ pub fn parse_loci(loci_list: &Vec<String>) -> HashSet<(String, u64, u64)> {
 
 pub fn parse_locus(locus: String) -> Result<(String, u64, u64)> {
     let l_fmt = locus.replace(",", "");
-    let parts: Vec<&str> = l_fmt.split(|c| (c == ':' || c == '-')).collect();
+    let parts1: Vec<&str> = l_fmt.split(|c| c == ':').collect();
+    let parts2: Vec<&str> = parts1[1].split(|c| c == '-').collect();
 
-    let chr = parts[0].to_string();
+    let chr = parts1[0].to_string();
 
-    if parts.len() == 2 {
-        let start = match parts[1].parse::<u64>() {
+    if parts2.len() == 1 {
+        let start = match parts2[0].parse::<u64>() {
             Ok(val) => val,
             Err(e) => {
                 return Err(anyhow::Error::new(e));
             }
         };
 
         Ok((chr, start - 1000, start + 1000))
-    } else if parts.len() == 3 {
-        let start = match parts[1].parse::<u64>() {
+    } else if parts2.len() == 2 {
+        let start = match parts2[0].parse::<u64>() {
             Ok(val) => val,
             Err(e) => {
                 return Err(anyhow::Error::new(e));
             }
         };
 
-        let stop = match parts[2].parse::<u64>() {
+        let stop = match parts2[1].parse::<u64>() {
             Ok(val) => val,
             Err(e) => {
                 return Err(anyhow::Error::new(e));