relaxed mode

10XGenomics · Dec 1, 2020 · 5251091 · 5251091
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commit 5251091
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Showing 4 changed files with 22 additions and 7 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "bamtofastq"
-version = "1.3.2"
+version = "1.3.3"
 authors = ["Patrick Marks <patrick@10xgenomics.com>"]
 edition = "2018"
 

diff --git a/src/main.rs b/src/main.rs
@@ -72,6 +72,7 @@ Options:
   --nthreads=<n>        Threads to use for reading BAM file [default: 4]
   --locus=<locus>       Optional. Only include read pairs mapping to locus. Use chrom:start-end format.
   --reads-per-fastq=N   Number of reads per FASTQ chunk [default: 50000000]
+  --relaxed             Skip unpaired or duplicated reads instead of throwing an error.
   --gemcode             Convert a BAM produced from GemCode data (Longranger 1.0 - 1.3)
   --lr20                Convert a BAM produced by Longranger 2.0
   --cr11                Convert a BAM produced by Cell Ranger 1.0-1.1
@@ -106,6 +107,7 @@ pub struct Args {
     flag_lr20: bool,
     flag_cr11: bool,
     flag_traceback: bool,
+    flag_relaxed: bool,
 }
 
 /// A Fastq record ready to be written
@@ -1103,7 +1105,7 @@ pub fn inner<R: bam::Read>(
             // BX-sorted case: get a selected set of BXs
             let bxi = bx_index::BxIndex::new(args.arg_bam)?;
             let bx_iter = BxListIter::from_path(args.flag_bx_list.unwrap(), bxi, bam)?;
-            proc_double_ended(bx_iter, formatter, fq, cache_size, false)
+            proc_double_ended(bx_iter, formatter, fq, cache_size, false, args.flag_relaxed)
         } else {
             // Standard pos-sorted case
             //let recs_convert_err = bam.records().map(|x| x.map_err(|e| e.into()));
@@ -1113,14 +1115,15 @@ pub fn inner<R: bam::Read>(
                 fq,
                 cache_size,
                 args.flag_locus.is_some(),
+                args.flag_relaxed,
             )
         }
     } else {
         if args.flag_bx_list.is_some() {
             // BX-sorted case: get a selected set of BXs
             let bxi = bx_index::BxIndex::new(args.arg_bam)?;
             let bx_iter = BxListIter::from_path(args.flag_bx_list.unwrap(), bxi, bam)?;
-            proc_double_ended(bx_iter, formatter, fq, cache_size, false)
+            proc_double_ended(bx_iter, formatter, fq, cache_size, false, args.flag_relaxed)
         } else {
             println!("entry");
             proc_single_ended(bam.records(), formatter, fq)
@@ -1134,6 +1137,7 @@ fn proc_double_ended<I, E>(
     mut fq: FastqManager,
     cache_size: usize,
     restricted_locus: bool,
+    relaxed: bool
 ) -> Result<Vec<(PathBuf, PathBuf, Option<PathBuf>, Option<PathBuf>)>, Error>
 where
     I: Iterator<Item = Result<Record, E>>,
@@ -1145,7 +1149,7 @@ where
 
     let total_read_pairs = {
         // Cache for efficiently finding local read pairs
-        let mut rp_cache = RpCache::new(cache_size);
+        let mut rp_cache = RpCache::new(cache_size, relaxed);
 
         // For chimeric read piars that are showing up in different places, we will write these to disk for later use
         let w: ShardWriter<SerFq, SerFqSort> =
@@ -1209,7 +1213,7 @@ where
         let mut item_vec = _item_vec?;
 
         // We're missing a read in the pair, and we would expect it.
-        if item_vec.len() != 2 && !restricted_locus {
+        if !relaxed && item_vec.len() != 2 && !restricted_locus {
             let header = std::str::from_utf8(&item_vec[0].rec.head).unwrap();
             let msg = format_err!("Didn't find both records for a paired end read. Is your BAM file complete?\nRead name of unpaired record: {}", header);
             return Err(msg);
@@ -1391,6 +1395,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let out_path_sets = super::go(args, Some(2)).unwrap();
@@ -1427,6 +1432,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let out_path_sets = super::go(args, Some(2)).unwrap();
@@ -1465,6 +1471,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let out_path_sets = super::go(args, Some(2)).unwrap();
@@ -1503,6 +1510,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let res = super::go(args, Some(2));
@@ -1526,6 +1534,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let res = super::go(args, Some(2));
@@ -1548,6 +1557,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let res = super::go(args, Some(2));
@@ -1571,6 +1581,7 @@ mod tests {
             flag_locus: None,
             flag_bx_list: None,
             flag_traceback: false,
+            flag_relaxed: false,
         };
 
         let out_path_sets = super::go(args, Some(2)).unwrap();

diff --git a/src/rpcache.rs b/src/rpcache.rs
@@ -8,13 +8,15 @@ use std::collections::HashMap;
 pub struct RpCache {
     pub cache_size: usize,
     pub cache: HashMap<Vec<u8>, Record>,
+    pub relaxed: bool,
 }
 
 impl RpCache {
-    pub fn new(cache_size: usize) -> RpCache {
+    pub fn new(cache_size: usize, relaxed: bool) -> RpCache {
         RpCache {
             cache: HashMap::new(),
             cache_size,
+            relaxed,
         }
     }
 
@@ -27,6 +29,8 @@ impl RpCache {
                 } else if old_rec.is_first_in_template() && rec.is_last_in_template() {
                     Some((old_rec, rec))
                 } else {
+                    if self.relaxed { return None; }
+
                     println!(
                         "Found invalid set of BAM record for qname: {}.",
                         String::from_utf8_lossy(rec.qname())