Add experimental seqair pileup backend

Cargo.toml

@@ -23,6 +23,9 @@ path = "src/lib/mod.rs"
 name = "perbase"
 path = "src/main.rs"
 
+[features]
+seqair-pileup = ["dep:seqair", "dep:seqair-types"]
+
 [dependencies]
 anyhow = "1.0.41"
 bio = "3.0.0"
@@ -39,6 +42,8 @@ lru_time_cache = "0.11.1"
 num_cpus = "1.13.0"
 rayon = "1.4.0"
 rust-htslib = {version = "0.51", default-features = false, features = ["libdeflate"]}
+seqair = { version = "0.1.0", optional = true }
+seqair-types = { version = "0.1.0", optional = true }
 rust-lapper = "1.0"
 serde = { version = "1.0.116", features = ["derive"] }
 smartstring = { version = "1.0.1", features = ["serde"] }

README.md

@@ -94,6 +94,17 @@ If the `--mate-fix` flag is passed, each position will first check if there are
 
 If the `--reference-fasta` is supplied, the `REF_BASE` field will be filled in. The reference must be indexed and match the BAM/CRAM header of the input.
 
+#### Experimental seqair pileup backend
+
+`base-depth` can optionally be built with an experimental seqair-backed pileup engine:
+
+```bash
+cargo build --release --features seqair-pileup
+perbase base-depth --seqair-pileup ./test/test.bam
+```
+
+The htslib-backed path remains the default. The seqair path currently requires `--ref-fasta` for CRAM input.
+
 The output can be compressed and indexed as follows:
 
 ```bash
@@ -173,6 +184,9 @@ FLAGS:
 
             **NOTE** If this is set it could result in duplicate output entries for regions that overlap. **NOTE** This
             may cause issues with downstream tooling.
+        --seqair-pileup
+            Use the experimental seqair-backed pileup engine
+
     -V, --version
             Prints version information
 

examples/par_granges_example.rs

@@ -3,9 +3,9 @@ use anyhow::Result;
 use perbase_lib::{
     par_granges::{self, RegionProcessor},
     position::pileup_position::PileupPosition,
-    read_filter::ReadFilter,
+    read_filter::{ReadFilter, ReadView},
 };
-use rust_htslib::bam::{self, Read, pileup::Alignment, record::Record};
+use rust_htslib::bam::{self, Read};
 use std::path::PathBuf;
 
 // To use ParGranges you will need to implement a [`RegionProcessor`](par_granges::RegionProcessor),
@@ -32,11 +32,11 @@ struct BasicReadFilter {
 impl ReadFilter for BasicReadFilter {
     // Filter reads based SAM flags and mapping quality, true means pass
     #[inline]
-    fn filter_read(&self, read: &Record, _alignment: Option<&Alignment>) -> bool {
+    fn filter_read<R: ReadView + ?Sized>(&self, read: &R) -> bool {
         let flags = read.flags();
-        (!flags) & &self.include_flags == 0
-            && flags & &self.exclude_flags == 0
-            && &read.mapq() >= &self.min_mapq
+        (!flags) & self.include_flags == 0
+            && flags & self.exclude_flags == 0
+            && read.mapq() >= self.min_mapq
     }
 }