pufferfish

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installing without root

13

Hello, I would like to test puffAligner but the installation fails with the wrong C++ compiler detected when following the installation instructions. It seems that cmake it is skipping my...

ksahlin

Pufferfish doesn't build within a conda environment (which has all the prerequisites) due to failed build of tslib from SeqLib

9

During `make` of pufferfish I'm getting the following error. You can see just above the error it does the presence and sanity checks for `zlib.h` and all good, so something...

hermidalc

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

2

Four suggestions based off of 8c24fb15335825bc54d3548db23009c1ca479711: 1. The "-h" or "--help" options get a strange error. If they aren't implemented, then shouldn't the tool complain "no such option exist" versus...

nh13

It appears that the Pufferfish indexer supports using a gzipped FASTA reference file as input. Add description to help that it can do this.

hermidalc

Hi! During compilation I got the following error: > /usr/bin/ld: cannot open output file cedar: Is a directory OS: Ubuntu 20.04.1 I solved simply by renaming the folder `cedar` to...

enricorox

[Here](https://github.com/COMBINE-lab/pufferfish/blob/develop/CMakeLists.txt#L429) and [here](https://github.com/COMBINE-lab/pufferfish/blob/develop/CMakeLists.txt#L398). It is more packaging-friendly to utilie what git can do and not download anything during build.

yurivict

Implementation of soft-clipping and CIGAR computation

2

Here is a short summary of the changes: - [x] Enabling soft-clipping * Proper use of KSW2 alignment results: Track the best scoring prefix alignment (during KSW2 extension) in addition...

haghshenas

Puffaligner doesn't map read pairs to different references

2

Hi, There are some applications where it's important to identify reads pairs where the reads map to different references. Even though Puffaligner map reads independently ("(…) *we consider the chaining...

apcamargo

[Question] Effect of the 'genomicReads' parameter

1

Hey! I got one question: the `pufferfish align` command has a `--genomicReads` parameter, which I assume activates a non-splice alignment mode. However the README says that spliced-alignment is not currently...

apcamargo

[Suggestion] Allow output to stdout

2

Currently, the only way to get a bam file from puffalign is to write a sam and then convert it in a separate command. If puffalign could output to stdout...

apcamargo