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use bigsi;
use build;
use read_id_mt_pe;
use reports;
use std::time::SystemTime;
pub fn read_id_batch(
batch_samples: &str,
index: &str,
threads: usize,
down_sample: usize,
fp_correct: f64,
batch: usize,
quality: u8,
bitvector_sample: usize,
high_mem_load: bool,
tag: &str,
) {
//tab to map to read batch
let batch_map = build::tab_to_map(batch_samples.to_string());
let bigsi_time = SystemTime::now();
if index.ends_with(".mxi") {
//let metadata = fs::metadata(&index).expect("Can't read metadata index!");
let bigsi = if high_mem_load {
bigsi::read_bigsi_mini_highmem(index)
} else {
bigsi::read_bigsi_mini(index)
};
match bigsi_time.elapsed() {
Ok(elapsed) => {
eprintln!("Index loaded in {} seconds", elapsed.as_secs());
}
Err(e) => {
// an error occurred!
eprintln!("Error: {:?}", e);
}
}
//start iterating through files here
for (accession, fq_vec) in &batch_map {
eprintln!("Classifying {}", accession);
let prefix = format!("{}_{}", accession, tag);
let mut fq: Vec<_> = vec![];
fq = fq_vec.iter().map(|r|{&r[..]}).collect();
if fq[0].ends_with(".gz") {
if fq.len() > 1 {
read_id_mt_pe::per_read_stream_pe(
fq,
&bigsi.map,
&bigsi.colors,
&bigsi.n_ref_kmers,
bigsi.bloom_size,
bigsi.num_hash,
bigsi.k_size,
bigsi.m_size,
threads,
down_sample,
fp_correct,
batch,
&prefix,
quality,
bitvector_sample,
)
} else {
read_id_mt_pe::per_read_stream_se(
fq,
&bigsi.map,
&bigsi.colors,
&bigsi.n_ref_kmers,
bigsi.bloom_size,
bigsi.num_hash,
bigsi.k_size,
bigsi.m_size,
threads,
down_sample,
fp_correct,
batch,
&prefix,
quality,
bitvector_sample,
)
};
} else {
read_id_mt_pe::stream_fasta(
fq,
&bigsi.map,
&bigsi.colors,
&bigsi.n_ref_kmers,
bigsi.bloom_size,
bigsi.num_hash,
bigsi.k_size,
bigsi.m_size,
threads,
down_sample,
fp_correct,
batch,
&prefix,
bitvector_sample,
);
}
reports::read_counts_five_fields(prefix.to_owned() + "_reads.txt", &prefix);
}
} else {
let bigsi = if high_mem_load {
bigsi::read_bigsi_highmem(index)
} else {
bigsi::read_bigsi(index)
};
match bigsi_time.elapsed() {
Ok(elapsed) => {
eprintln!("Index loaded in {} seconds", elapsed.as_secs());
}
Err(e) => {
// an error occurred!
eprintln!("Error: {:?}", e);
}
}
for (accession, fq_vec) in &batch_map {
eprintln!("Classifying {}", accession);
let prefix = format!("{}_{}", accession, tag);
let mut fq: Vec<_> = vec![];
fq = fq_vec.iter().map(|r|{&r[..]}).collect();
if fq[0].ends_with(".gz") {
if fq.len() > 1 {
read_id_mt_pe::per_read_stream_pe(
fq,
&bigsi.map,
&bigsi.colors,
&bigsi.n_ref_kmers,
bigsi.bloom_size,
bigsi.num_hash,
bigsi.k_size,
0,
threads,
down_sample,
fp_correct,
batch,
&prefix,
quality,
bitvector_sample,
)
} else {
read_id_mt_pe::per_read_stream_se(
fq,
&bigsi.map,
&bigsi.colors,
&bigsi.n_ref_kmers,
bigsi.bloom_size,
bigsi.num_hash,
bigsi.k_size,
0,
threads,
down_sample,
fp_correct,
batch,
&prefix,
quality,
bitvector_sample,
)
};
} else {
read_id_mt_pe::stream_fasta(
fq,
&bigsi.map,
&bigsi.colors,
&bigsi.n_ref_kmers,
bigsi.bloom_size,
bigsi.num_hash,
bigsi.k_size,
0,
threads,
down_sample,
fp_correct,
batch,
&prefix,
bitvector_sample,
);
}
reports::read_counts_five_fields(prefix.to_owned() + "_reads.txt", &prefix);
}
}
}