fix: split bams no working as intended

rhysnewell · May 3, 2023 · 2bf7cdb · 2bf7cdb
1 parent ad89c5e
commit 2bf7cdb
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/src/processing/bams/index_bams.rs b/src/processing/bams/index_bams.rs
@@ -110,7 +110,10 @@ fn split_bams_to_references<R: NamedBamReader>(
     let mut record: bam::Record = bam::Record::new();
 
     while bam_generator.read(&mut record).is_some() {
-        let record_tid = record.tid() as usize;
+        let record_tid = record.tid();
+        if record_tid < 0 {
+            continue;
+        }
         let ref_name = std::str::from_utf8(bam_generator.header().tid2name(record_tid as u32)).expect("Cannot read reference name from bam file").split('~').next().unwrap();
 
         let writer = bam_writer_map.get_mut(ref_name).unwrap();

diff --git a/src/reference/reference_reader_utils.rs b/src/reference/reference_reader_utils.rs
@@ -202,11 +202,10 @@ impl ReferenceReaderUtils {
     }
 
     pub fn generate_faidx(reference_path: &str) -> IndexedReader<File> {
-        external_command_checker::check_for_samtools();
         // debug!("Generating reference index");
         let cmd_string = format!(
             "set -e -o pipefail; \
-                     samtools faidx {}",
+            samtools faidx {}",
             reference_path
         );
         // debug!("Queuing cmd_string: {}", cmd_string);
@@ -216,7 +215,8 @@ impl ReferenceReaderUtils {
             // debug!("Found existing index file at {}", fai_path);
             return IndexedReader::from_file(&reference_path).expect("Unable to generate index");
         }
-
+
+        external_command_checker::check_for_samtools();
         std::process::Command::new("bash")
             .arg("-c")
             .arg(&cmd_string)