2024/10/28-11:02:53 (Linux VDI0092.zit.bam.de x86_64)

pbenner · Oct 28, 2024 · 8838a3e · 8838a3e
1 parent d1b0414
commit 8838a3e
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diff --git a/README.md b/README.md
@@ -72,15 +72,14 @@ use crate::granges::GRanges;
 let granges = GRanges::import_gtf("src/granges_gtf.gtf",
     vec!["gene_id", "gene_num"], // Names of optional fields
     vec!["str"    , "int"     ], // Types of optional fields
-    vec![]
+    vec![None     , Some("0") ], // Default values, can be an empty vector if omitted
 ).unwrap();
-
 ```
 The result is:
 ```bash
   seqnames ranges         strand |                             source    feature gene_num         gene_id
 1 1        [11869, 14409) +      | transcribed_unprocessed_pseudogene       gene        1 ENSG00000223972
-2 1        [11870, 14410) +      |               processed_transcript transcript        2 ENSG00000223972
+2 1        [11870, 14410) +      |               processed_transcript transcript        0 ENSG00000223972
 ```
 
 ### Read a BAM file into a GRanges object

diff --git a/src/granges_gtf.gtf b/src/granges_gtf.gtf
@@ -1,2 +1,2 @@
 1 transcribed_unprocessed_pseudogene  gene        11869 14409 . + . gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; gene_num "1"; 
-1 processed_transcript                transcript  11870 14410 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; gene_num "2";
+1 processed_transcript                transcript  11870 14410 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";
diff --git a/src/granges_gtf.rs b/src/granges_gtf.rs
@@ -492,7 +492,7 @@ mod tests {
         let granges = GRanges::import_gtf("src/granges_gtf.gtf",
             vec!["gene_id", "gene_num"], // Names of optional fields
             vec!["str"    , "int"     ], // Types of optional fields
-            vec![]
+            vec![None     , Some("0") ], // Default values, can be an empty vector if omitted
         ).unwrap();
 
         assert_eq!(granges.num_rows(), 2);