Skip QUAL, update flate2

BimberLab · Jan 18, 2025 · 8930507 · 8930507
1 parent 3257af9
commit 8930507
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/Cargo.toml b/Cargo.toml
@@ -26,7 +26,7 @@ array_tool = "1.0.3"
 unwrap = "1.2.1"
 niffler = "2.2.0"
 rust-htslib = "0.40.2"
-flate2 = "1.0.22"
+flate2 = "1.0.35"
 lexical-sort = "0.3.1"
 rayon = "1.7.0"
 rand = "0.8.5"

diff --git a/src/parse/bam.rs b/src/parse/bam.rs
@@ -22,7 +22,7 @@ pub const BAM_FIELDS_TO_REPORT: [&'static str; 37] = [
     "MAPQ",
     "POS",
     "MATE_POS",
-    "SEQ", // This gets filtered out before getting written to disk in the bam processingm it's just used for associating reads to filter info
+    "SEQ",
     "SEQ_LEN",
     "INSERT_SIZE",
     //"CIGAR",

diff --git a/src/process/bam.rs b/src/process/bam.rs
@@ -23,6 +23,7 @@ fn bam_data_values(bam_data: &Vec<String>) -> String {
     bam_data
         .iter()
         .enumerate() 
+        .filter(|&(index, _)| index != 1) 
         .filter(|&(index, _)| index != 15) 
         .map(|(_, value)| value.as_str())
         .collect::<Vec<&str>>()
@@ -33,6 +34,7 @@ fn bam_data_header(prefix: &str) -> String {
     BAM_FIELDS_TO_REPORT
         .iter()
         .enumerate() 
+        .filter(|&(index, _)| index != 1) 
         .filter(|&(index, _)| index != 15) 
         .map(|(_, &field)| format!("{}_{}", prefix, field))
         .collect::<Vec<String>>()