Rename Piped to InThread, and add decode_in_thread

Author: willchet

CHANGELOG.md

@@ -17,6 +17,9 @@ is roughly based on [Keep a Changelog], and this project tries to adheres to
   connected components. Phase labels are now ordered deterministically by
   cluster size (descending), lowest variant position, then lowest minority
   allele byte value.
+- Renamed `GzipReaderPiped` to `GzipReaderInThread` and altered API for it
+- Renamed `ReadFileZipPipe` to `ReadFileZipInThread`
+- `use_file_or_zip_threaded` has been removed in favor of a separate `decode_in_thread` method
 
 ## Fixed
 

crates/irma-core-cli/processes/integrated/preprocess/mod.rs

@@ -10,7 +10,7 @@ use clap::{Args, ValueHint};
 use foldhash::fast::SeedableRandomState;
 use irma_records::{
     fastq::ReadTransforms,
-    io::{InputOptions, IterWithContext, OutputOptions, ReadFileZipPipe, RecordReaders, WriterWithContext},
+    io::{InputOptions, IterWithContext, OutputOptions, ReadFileZipInThread, RecordReaders, WriterWithContext},
     {
         hashing::get_hasher,
         paired::{ReadSide, ZipPairedReadsError, ZipPairedReadsExt},
@@ -111,7 +111,7 @@ pub fn preprocess_process(args: PreprocessArgs) -> Result<(), std::io::Error> {
 /// context.
 struct Reader {
     path: PathBuf,
-    iter: IterWithContext<FastQReader<ReadFileZipPipe>>,
+    iter: IterWithContext<FastQReader<ReadFileZipInThread>>,
 }
 
 struct ParsedPreprocessIoArgs {
@@ -152,7 +152,8 @@ fn parse_preprocess_args(args: PreprocessArgs) -> std::io::Result<ParsedPreproce
     } = args;
 
     let readers = InputOptions::new_from_paths(&fastq_input, fastq_input2.as_ref())
-        .use_file_or_zip_threaded()
+        .use_file_or_zip()
+        .decode_in_thread()
         .parse_fastq()
         .open()?;
 

crates/irma-core-cli/processes/standalone/aligner/arg_parsing.rs

@@ -109,7 +109,8 @@ pub fn parse_aligner_args(args: AlignerArgs) -> std::io::Result<ParsedAlignerArg
     }
 
     let query_reader = InputOptions::new_from_path(&args.query_file)
-        .use_file_or_zip_threaded()
+        .use_file_or_zip()
+        .decode_in_thread()
         .parse_fastx()
         .open()?;
 

crates/irma-core-cli/processes/standalone/aligner/mod.rs

@@ -3,7 +3,7 @@ use crate::aligner::{
     writers::{AlignmentWriter, write_header},
 };
 use clap::{Args, builder::RangedI64ValueParser};
-use irma_records::io::{FastX, FastXReader, IterWithContext, OutputOptions, ReadFileZipPipe};
+use irma_records::io::{FastX, FastXReader, IterWithContext, OutputOptions, ReadFileZipInThread};
 use std::{cmp::Ordering, io::Write, path::PathBuf, sync::atomic::AtomicU64};
 use zoe::{
     alignment::{Alignment, LocalProfiles, MaybeAligned, SharedProfiles, sw::max_score_for_int_type},
@@ -20,7 +20,7 @@ mod arg_parsing;
 mod writers;
 
 /// A type alias for the query reader used by `aligner`.
-type QueryReader = IterWithContext<FastXReader<ReadFileZipPipe>>;
+type QueryReader = IterWithContext<FastXReader<ReadFileZipInThread>>;
 
 /// A type alias for the writer being used for the SAM file, which depends on
 /// whether `dev_no_rayon` is set.

crates/irma-core-cli/processes/standalone/sampler.rs

@@ -3,7 +3,7 @@
 use clap::Args;
 use irma_records::{
     io::{
-        DispatchFastX, FastXReader, InputOptions, IterWithContext, OutputOptions, ReadFileZipPipe, RecordReaders,
+        DispatchFastX, FastXReader, InputOptions, IterWithContext, OutputOptions, ReadFileZipInThread, RecordReaders,
         RecordWriters, SequenceWriter, WriteFileZipStdout, WriteRecord, WriteRecordCompatibleItem, WriteRecords,
         check_distinct_files, is_gz,
     },
@@ -365,7 +365,7 @@ fn get_paired_seq_count(io_args: &IOArgs) -> std::io::Result<Option<usize>> {
 /// context.
 struct Reader {
     path: PathBuf,
-    iter: IterWithContext<FastXReader<ReadFileZipPipe>>,
+    iter: IterWithContext<FastXReader<ReadFileZipInThread>>,
 }
 
 /// The IO arguments used by sampler, including up to two readers and writers.
@@ -398,7 +398,8 @@ fn parse_sampler_args(args: SamplerArgs) -> Result<(IOArgs, Xoshiro256StarStar,
     )?;
 
     let readers = InputOptions::new_from_paths(&args.input_file, args.input_file2.as_ref())
-        .use_file_or_zip_threaded()
+        .use_file_or_zip()
+        .decode_in_thread()
         .parse_fastx()
         .open()?;
 

crates/irma-core-cli/processes/standalone/trimmer.rs

@@ -8,7 +8,7 @@ use clap::Args;
 use core::fmt;
 use irma_records::{
     io::{
-        InputOptions, IterWithContext, OutputOptions, PairedWriters, ReadFileZipPipe, RecordWriters, WriteFileZipStdout,
+        InputOptions, IterWithContext, OutputOptions, PairedWriters, ReadFileZipInThread, RecordWriters, WriteFileZipStdout,
         WriteRecord, check_distinct_files,
     },
     paired::{DeinterleavedPairedReadsExt, ZipPairedReadsExt, ZipReadsError},
@@ -311,7 +311,7 @@ impl fmt::Display for PairedIoStrategy {
 
 /// Parsed arguments for the `trimmer` subprocess
 struct ParsedTrimmerArgs {
-    io_args:       PairedIoArgs<IterWithContext<FastQReader<ReadFileZipPipe>>, WriteFileZipStdout>,
+    io_args:       PairedIoArgs<IterWithContext<FastQReader<ReadFileZipInThread>>, WriteFileZipStdout>,
     strategy:      PairedIoStrategy,
     trimming_args: ParsedTrimmerOptions,
     primer_file:   Option<PathBuf>,
@@ -351,7 +351,8 @@ fn parse_trimmer_args(args: TrimmerArgs) -> std::io::Result<ParsedTrimmerArgs> {
     check_distinct_files(&fastq_input, fastq_input2.as_ref(), output.as_ref(), output2.as_ref())?;
 
     let readers = InputOptions::new_from_paths(&fastq_input, fastq_input2.as_ref())
-        .use_file_or_zip_threaded()
+        .use_file_or_zip()
+        .decode_in_thread()
         .parse_fastq()
         .open()?;
 

crates/irma-core-cli/processes/standalone/xleave.rs

@@ -34,7 +34,8 @@ pub fn xleave_process(args: XleaveArgs) -> Result<(), std::io::Error> {
     )?;
 
     let readers = InputOptions::new_from_paths(&args.input_file1, args.input_file2.as_ref())
-        .use_file_or_zip_threaded()
+        .use_file_or_zip()
+        .decode_in_thread()
         .parse_fastx()
         .open()?;