Only emit paired-end reads

Author: kvg

src/hidive/src/rescue.rs

@@ -849,20 +849,20 @@ fn write_paired_fastq_records(records: &[BamRecord], fastq_writer: &mut fastq::W
 
     for (qname, records) in grouped_records {
         if records.len() == 1 {
-            // Handle singleton reads
-            let record = records[0];
-            if record.is_reverse() {
-                let rv_seq = record.seq().as_bytes().reverse_complement();
-                let mut rv_qual = record.qual().iter().map(|&q| q + 33).collect::<Vec<u8>>();
-                rv_qual.reverse();
-                let rv_record = fastq::Record::with_attrs(&String::from_utf8_lossy(record.qname()), None, &rv_seq, &rv_qual);
-                fastq_writer.write_record(&rv_record).unwrap();
-            } else {
-                let fw_seq = record.seq().as_bytes();
-                let fw_qual = record.qual().iter().map(|&q| q + 33).collect::<Vec<u8>>();
-                let fw_record = fastq::Record::with_attrs(&String::from_utf8_lossy(record.qname()), None, &fw_seq, &fw_qual);
-                fastq_writer.write_record(&fw_record).unwrap();
-            }
+            // // Handle singleton reads
+            // let record = records[0];
+            // if record.is_reverse() {
+            //     let rv_seq = record.seq().as_bytes().reverse_complement();
+            //     let mut rv_qual = record.qual().iter().map(|&q| q + 33).collect::<Vec<u8>>();
+            //     rv_qual.reverse();
+            //     let rv_record = fastq::Record::with_attrs(&String::from_utf8_lossy(record.qname()), None, &rv_seq, &rv_qual);
+            //     fastq_writer.write_record(&rv_record).unwrap();
+            // } else {
+            //     let fw_seq = record.seq().as_bytes();
+            //     let fw_qual = record.qual().iter().map(|&q| q + 33).collect::<Vec<u8>>();
+            //     let fw_record = fastq::Record::with_attrs(&String::from_utf8_lossy(record.qname()), None, &fw_seq, &fw_qual);
+            //     fastq_writer.write_record(&fw_record).unwrap();
+            // }
         } else {
             // Handle paired reads
             let mut paired_records = Vec::new();

wdl/RescueAndLocityper.wdl

@@ -115,6 +115,49 @@ task SubsetVCF {
     }
 }
 
+task GenerateDBFromVCF {
+    input {
+        File reference
+        File reference_index
+        File counts_jf
+        File vcf
+        String docker
+    }
+
+    Int disk_size = 10
+    String output_tar = "db.tar.gz"
+
+    command <<<
+        set -euxo pipefail
+
+        gunzip -c ~{reference} > reference.fa
+        samtools faidx reference.fa
+
+        locityper add -d db \
+            -r reference.fa \
+            -j ~{counts_jf} \
+            -l ~{locus_name} ~{locus_coordinates} ~{alleles_fa}
+
+        find ~{locus_name}.db -type f -exec ls -lah {} \;
+        
+        echo "compressing DB"
+        tar -czf ~{output_tar} ~{locus_name}.db
+        echo "done compressing DB"
+    >>>
+
+    runtime {
+        memory: "8 GB"
+        cpu: "1"
+        disks: "local-disk " + disk_size + " HDD"
+        preemptible: 3
+        docker: docker
+    }
+
+    output {
+        File db_tar = output_tar
+    }
+}
+
 task GenerateDB {
     input {
         File reference