Fatemeh Almodaresi comments

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                                            Fatemeh Almodaresi

[Question] Effect of the 'genomicReads' parameter

Hi @apcamargo , Thanks for the question. As the readme says, currently Puffaligner does not support spliced-alignment. The flag `--genomicReads` is mainly put for metagenomic alignments. The only difference it...

Improve the help message, remove duplicate option descriptions, and get clarify options with the same flag

Dear Nils (@nh13 ), Thank you for your quick test of PuffAligner. The particular items you pointed at in this issue are definitely something that requires our immediate action to...

Align without the "-o" option should just output to standard output

If you run it with `-o -` it will output to standard output, but I think we'd better just remove that requirement as you said.

Support interleaved paired end FASTQs

Dear Nils (@nh13), Thank you for your quick test of PuffAligner. We appreciate all your useful feedback about making PuffAligner easier to use. Support for interleaved FASTQ files seems as...

Puffaligner doesn't map read pairs to different references

Hi @apcamargo , Thank you for your post. However, I am not sure if I understand the request clearly. Would you mind explaining a little bit more?

Relative tmp address

Thanks @rchikhi , you're right. It has the mode. But I thought this makes it use maximum memory and we would like to limit memory usage by allowing intermediate disk...

failure compiling Pufferfish, a dependency of Agamemnon

Hi @ponomarevsy , So if I'm correct, you still are able to install the package, but it doesn't go through your TBB binary. right?

failure compiling Pufferfish, a dependency of Agamemnon

Thank you @ponomarevsy , I see that it has not been able to install bz2 and lzma as well. Just a few things to check with you: 1. you are...