Usage

$ markerIndices=marker1,marker2,... \
  minScores=score1,score2,... \
  demultiplex.sh \
    removeDuplicates_file

---
title: demultiplex.sh
---
flowchart TD
    UNIQUE[(
        removeDuplicates_file
        
            
                R1
                R2
                ...
                #
            
            
                ...
                ...
                ...
                ...
            
        
    )]
    UNIQUE --> DM[demultiplex.sh]
    MK1[(marker1)] --> DM
    MK2[(marker2)] --> DM
    MKN[(...)] --> DM
    SCORE[(
        minScores
        
            
                score1
                score2
                ...
            
            
                ...
                ...
                ...
            
        
    )]
    SCORE --> DM
    DM --> ONTARGET[(
        stdout
        
            
                R1
                R2
                ...
                #
                id
                rstart1
                rend1
                qstart1
                qend1
                rstart2
                rend2
                qstart2
                qend2
                ...
            
            
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
                ...
            
        
    )]

R1	R2	...	#
...	...	...	...

score1	score2	...
...	...	...

R1	R2	...	#	id	rstart1	rend1	qstart1	qend1	rstart2	rend2	qstart2	qend2	...
...	...	...	...	...	...	...	...	...	...	...	...	...	...

markerN is bowtie2 index of a fasta file containing possible alignment targets of RN.
scoreN is feed to bowtie2 to filter alignments with low scores. The alignments are in local mode instead of end-to-end mode, and there is no reverse complement. The full alignment setting is
```
--norc --local -L 15 --ma 1 --mp 2,2 --rdg 3,1 --rfg 3,1 --score-min C,scoreN
```
The fasta name of marker1 and marker2 must the 0-based reference id, see the core part of rearr.
R1 and R2 are given in removeDuplicates_file, which is stdout of removeDuplicates.sh.
demultiplex.sh only output a row in removeDuplicates_file only of both R1 and R2 aligned to targets with consistant reference id.
R1, R2 and # are copied from removeDuplicates_file.
rstartN and rendN denotes the left-close-right-open 0-based range of the aligned part of the target of RN. qstartN and qendN denotes that of RN.
Multiple marker (more than two) are supported in theory.

Source

mapMarker()
{
    # Usage: mapMarker minScore markerIndex <reads
    # Map reads to marker by bowtie2
    # Input: plain reads
    # Output: sam file without header
    minScore=$1
    markerIndex=$2
    bowtie2 --quiet --mm --norc --local -L 15 --ma 1 --mp 2,2 --rdg 3,1 --rfg 3,1 --score-min C,${minScore} -r -x "${markerIndex}" -U - 2>/dev/null | samtools view
}

filterMarkers()
{
    # Input: seq1|seq2|...|count|flag1|refId1|markerStart1|markerEnd1|seqStart1|seqEnd1|flag2|refId2|markerStart2|markerEnd2|seqStart2|seqEnd2|...
    # Output: seq1|seq2|...|count|refId|markerStart1|markerEnd1|seqStart1|seqEnd1|markerStart2|markerEnd2|seqStart2|seqEnd2|...
    # filter out rows with one of the following happens:
    # 1. seqN failed to align markerIndexN
    # 2. refIdM != refIdN for some M and N
    gawk -F "\t" -v OFS="\t" -v firstFlagPos=$((${#markerIndexArray[@]}+2)) '
        {
            refId = $(firstFlagPos+1)
            for (i = firstFlagPos; i <= NF; i += 6) {
                if ($i != 0 || $(i+1) != refId) {
                    next
                }
            }
            for (i = 1; i < firstFlagPos; ++i) {
                printf("%s\t", $i)
            }
            printf("%s\t", $(firstFlagPos+1))
            for (i = firstFlagPos; i < NF; ++i) {
                if ((i - firstFlagPos) % 6 <= 1) {
                    continue
                }
                printf("%s\t", $i)
            }
            printf("%s\n", $NF)
        }
    '
}

inputFile=$1

IFS=',' read -r -a markerIndexArray <<< "${markerIndices}"
IFS=',' read -r -a minScoreArray <<< "$minScores"
maps=""
for ii in ${!markerIndexArray[@]}
do
    maps="${maps} <(cut -f$((ii+1)) ${inputFile} | mapMarker ${minScoreArray[$ii]} ${markerIndexArray[$ii]} | gawk -f getAlignPos.awk)"
done

eval paste "${inputFile}" $maps | filterMarkers

alias ~~~=":" # This suppresses a warning and is not part of source.