#!/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 \
| minimap2 -t 20 -K 100k -ax map-ont $TRANSCRIPTOME -  2>/dev/null| samtools view -b \
| seqkit bam  -B 3 -f IsSec -W 4 -x -p 4000 \
| seqkit bam -Q -m 1 -x -p 600000 -c $COUNT_TSV -e "$COUNT_MONITOR" \
| samtools sort -o sorted_aln.bam -
samtools index sorted_aln.bam;