Async reader (#6)

* add async support

* revise the user interface

* allow input from url when possible

.gitignore

@@ -1,5 +1,6 @@
 target
 *.gz
+*.zst
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

docs/api.rst

@@ -32,4 +32,5 @@ Utilities
 .. autosummary::
     :toctree: _autosummary
 
-    utils.strip_barcode_from_fastq
+    utils.strip_barcode_from_fastq
+    bam_to_fastq

precellar/Cargo.toml

@@ -6,15 +6,15 @@ edition = "2021"
 [dependencies]
 anyhow = "1.0"
 bed-utils = "0.5.1"
-bwa-mem2 = { git = "https://github.com/regulatory-genomics/bwa-mem2-rust.git", rev = "07eda9b9c2815ae52b3fa30b01de0e19fae31fe0" }
-star-aligner = { git = "https://github.com/regulatory-genomics/star-aligner", rev = "f9915ea3afbac1e8f4773e2e7c22376f1549c3c7" }
+bwa-mem2 = { git = "https://github.com/regulatory-genomics/bwa-mem2-rust.git", rev = "8de06bcc0a2145fd819232ffb2bf100fb795db30" }
+star-aligner = { git = "https://github.com/regulatory-genomics/star-aligner", rev = "faef1085eaf26e6e8d5875fcbc641c3af9444d89" }
 bstr = "1.0"
 either = "1.13"
 itertools = "0.13"
 indexmap = "2.5"
 log = "0.4"
 lexical = "6.1"
-noodles = { version = "0.80", features = ["core", "fastq", "bam", "sam", "async"] }
+noodles = { version = "0.85", features = ["core", "fastq", "bam", "sam", "async"] }
 kdam = "0.5.2"
 rayon = "1.10"
 smallvec = "1.13"