Enable mapping TELL-Seq and DBS linked reads

[pontushojer]

This PR extends the ema align tool too allow mapping of both TELL-Seq and DBS linked reads.

[pdimens]

Thanks for submitting this, awesome! While I'm not one of the ema devs, I was granted collaboration rights to merge PRs. Do you have tests/records confirming this PR hasn't broken anything?

[pontushojer]

I have run tests with ema align using subsets of 10x, TELL-Seq and DBS reads to confirm that things look ok. Not Haplotagging though, do you perhaps have some small test set you could send me?

I would probably be good to add some kind of basic testing suite to this repo.

[pdimens]

Included is 20 each of forward and reverse haplotag reads for testing purposes:
https://mega.nz/folder/CEp3wSYA#3_LCUTz7S5YP0UazieFbDg

[pontushojer]

Thanks for sending the files!

I tried using the files but I am unable to get any output, including when running on the current master branch 1d3b65d! Maybe I am not using the command correctly for haplotag reads. This is the command that I am running:

./ema align -p haplotag -1 <(pigz -cd haplotag.F.fq.gz) -2 <(pigz -cd haplotag.F.fq.gz) -r ref.fasta

This is the output:

stdout

@HD	VN:1.3	SO:unsorted
@SQ	SN:chrA	LN:50000
@SQ	SN:chrB	LN:40000
@SQ	SN:chrC	LN:9000
@SQ	SN:chrD	LN:1000
@RG	ID:rg1	SM:sample1
@PG	ID:ema	PN:ema	VN:0.6.2	CL:./ema align -p haplotag -1 /dev/fd/63 -2 /dev/fd/62 -r ref.fasta

stderr

BWA initialization...
[M::bwa_idx_load_from_disk] read 0 ALT contigs
Processing reads...

It only generates the header, no alignments.

On another note, it would be good to have a bit of a larger test set with multiple reads per barcode. The current files contain only one read pair per barcode which would then skip most of ema's remapping functionality. Also it would be good to have a known reference which they should map to. I have generate testdata for a subsection of GRCh38 chr1 which i used for testing the other technologies.

[pdimens]

Sorry about that, I used a minimal set for simplicity. I'll aim for a bigger file and send those links

[pdimens]

Try the files now. I replaced them with subsets featuring 1.6M reads apiece.

[pontushojer]

@pdimens I have now run the tests using the haplotag reads you provided. I had to make one change but now the output from this PR matches master for haplotag reads.

[pdimens]

I saw the new issues you posted. Unfortunately, I'm both inexperienced with C++ and not one of the ema devs. The points you make are quite serious, but I am unable to modify ema to overcome these issues. I was given collaboration rights to merge PRs, but you should try pinging @arshajii

[pontushojer]

I saw the new issues you posted. Unfortunately, I'm both inexperienced with C++ and not one of the ema devs. The points you make are quite serious, but I am unable to modify ema to overcome these issues. I was given collaboration rights to merge PRs, but you should try pinging @arshajii

As ema devs, I would guess they already get notifications on this. I am also too inexperienced in C/C++ to make any attempt to fix this.

This PR is however unrelated to the issues I raised. On my end it is ready to merge. What do you think?