bsipos

#!/bin/bash -
set -o nounset
for i in `seq 1 100`;
do
    start=`date +%N`; 
    grep -c "^+$" test.fq >/dev/null; 
    end=`date +%N`; 
    TS=`expr $end - $start`;
    TM=`echo $TS/1000.0 | bc -l`
    echo -e "grep\t1\t$TM" >> count_timing.tsv;

bsipos

#!/bin/bash -
set -o nounset                              # Treat unset variables as an error

TSV="count_timing.tsv"
CORES=2
TAGS=$1

echo -n "" > test.fq
for c in `seq 1 32`; do cat ../tests/pcs109_5k.fq >> test.fq; done
echo -e "Group\tBuffSize\tTime" > $TSV

bsipos

#!/bin/bash -
set -o nounset                              # Treat unset variables as an error

TSV="big_count_timing.tsv"
CORES=2
TAGS="lines exact-buff buff-readahead"

echo -n "" > test.fq
for c in `seq 1 128`; do cat ../tests/pcs109_5k.fq >> test.fq; done
echo -e "Group\tBuffSize\tTime" > $TSV

bsipos

// bufio
import "github.com/klauspost/readahead"
// ...
// Create new readahead buffered reader:
reader, err := readahead.NewReaderSize(fh, 100, buffSize)
checkError(err)
// ...

bsipos

// CountFastxRecords counts the number of records in a fastx file.
func CountFastxRecords(fh *os.File, buffSize int, format string) int {
	// Start the timer:
	start := time.Now()
	pattern := []byte{'\n', '+', '\n'} // Pattern to look for.
	// Create new buffered reader:
	reader := bufio.NewReaderSize(fh, buffSize)
	// Byte buffer:
	buffer := make([]byte, buffSize)
	// Auxiliary buffer:

bsipos

// CountFastxRecords counts the number of records in a fastx file.
func CountFastxRecords(fh *os.File, buffSize int, format string) int {
        // Start the timer:
        start := time.Now()
        pattern := []byte("\n+\n") // Pattern to look for.
        // Create new buffered reader:
        reader := bufio.NewReaderSize(fh, buffSize)
        // Byte buffer:
        buffer := make([]byte, buffSize)
        // Variable for counting records:

bsipos

#!/bin/bash -
set -o nounset                              # Treat unset variables as an error

TSV="count_timing.tsv"
CORES=4
echo "Time" > $TSV
for i in `seq 1 10000`
do
        seqkit -j $CORES count pcs109_5k.fq 1>/dev/null 2>> $TSV
done

bsipos

// CountFastxRecords counts the number of records in a fastx file.
func CountFastxRecords(fh *os.File, buffSize int, format string) int {
        // Start the timer:
        start := time.Now()
        pattern := "+\n" // Pattern to look for.
        // Create new buffered reader:
        reader := bufio.NewReaderSize(fh, buffSize)
        // Variable for counting records:
        var records int

bsipos

func CountFastxRecords(fh *os.File, buffSize int, format string) int {
        // Do the counting here.
        return 0
}

bsipos

#!/bin/bash

INPUT_FQ=demo_reads.fq
TRANSCRIPTOME="transcriptome.fas"
COUNT_TSV="online_counts.tsv"
COUNT_MONITOR="[ -f $COUNT_TSV ] && ( csvtk -t watch -O sec_dist.pdf -B 100 -f SecCount $COUNT_TSV ; sleep 2)" # script to monitor secondary read count distribution

csvtk cat $INPUT_FQ \
| seqkit seq -Q 3 \
| seqkit watch -x -f MeanQual -p 20000 \