[feature] Add bgzf support

CHANGELOG.md

@@ -1,5 +1,10 @@
 # Changelog
 
+## v0.6.2
+
+- Output BGZF output by default, which can be indexed and queried with tabix
+- Read input gzipped files a `MultiGzDecoder` which is more flexible
+
 ## v0.6.1
 
 - PGO build fix

Cargo.toml

@@ -28,7 +28,7 @@ anyhow = "1.0.41"
 bstr = "0.2.16"
 env_logger = "0.8.4"
 flate2 = { version = "1.0", features = ["zlib-ng-compat"], default-features = false }
-gzp = {version = "0.7.1", default-features = false, features = ["deflate_zlib_ng"]}
+gzp = {version = "0.8.0", default-features = false, features = ["deflate_zlib_ng","libdeflate"]}
 grep-cli = "0.1.6"
 lazy_static = "1.4.0"
 log = "0.4.14"

README.md

@@ -23,6 +23,7 @@ It is meant to be simple and easy to use while exploring datasets.
 - Selection of columns by header string literal with the `-F` option, or by regex by setting the `-r` flag
 - Input files will be automatically decompressed if their file extension is recognizable and a local binary exists to perform the decompression (similar to ripgrep). See [Decompression](#decompression).
 - Output can be gzip compressed using the multi-threaded compressors from [`gzp`](https://github.com/sstadick/gzp) with `-Z` flag
+  - This gzipped output is in BGZF format and can be indexed and queried with `tabix`
 - Exclude fields by index or by header.
 - Speed
 

src/lib/core.rs

@@ -11,7 +11,7 @@ use crate::{
 };
 use anyhow::Result;
 use bstr::ByteSlice;
-use flate2::read::GzDecoder;
+use flate2::read::MultiGzDecoder;
 use grep_cli::DecompressionReaderBuilder;
 use memchr;
 use regex::bytes::Regex;
@@ -103,7 +103,7 @@ impl<'a> CoreConfig<'a> {
                         .map(|p| p.ends_with(".gz"))
                         .unwrap_or(false)
                     {
-                        Box::new(GzDecoder::new(File::open(&path)?))
+                        Box::new(MultiGzDecoder::new(File::open(&path)?))
                     } else {
                         Box::new(
                             DecompressionReaderBuilder::new()
@@ -371,7 +371,7 @@ where
                     self.hck_bytes(header.as_bytes(), &mut output)?;
                 }
                 let reader: Box<dyn Read> = if self.config.try_decompress {
-                    Box::new(GzDecoder::new(io::stdin()))
+                    Box::new(MultiGzDecoder::new(io::stdin()))
                 } else {
                     Box::new(io::stdin())
                 };
@@ -389,7 +389,7 @@ where
                         .map(|p| p.ends_with(".gz"))
                         .unwrap_or(false)
                     {
-                        Box::new(GzDecoder::new(File::open(&path)?))
+                        Box::new(MultiGzDecoder::new(File::open(&path)?))
                     } else {
                         Box::new(
                             DecompressionReaderBuilder::new()

src/main.rs

@@ -2,7 +2,7 @@ use anyhow::{Context, Error, Result};
 use env_logger::Env;
 use flate2::Compression;
 use grep_cli::stdout;
-use gzp::{deflate::Gzip, ZBuilder};
+use gzp::{deflate::Bgzf, ZBuilder};
 use hcklib::{
     core::{Core, CoreConfig, CoreConfigBuilder, HckInput},
     field_range::RegexOrStr,
@@ -194,7 +194,7 @@ fn main() -> Result<()> {
     // TODO: Support all flate2 compression targets via enum on `-Z`
     let mut writer: Box<dyn Write> = if opts.try_compress {
         Box::new(
-            ZBuilder::<Gzip, _>::new()
+            ZBuilder::<Bgzf, _>::new()
                 .compression_level(Compression::new(opts.compression_level))
                 .num_threads(opts.compression_threads)
                 .from_writer(writer),