RapMap

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-u always active, unaligned reads cause parse error in samtools

2

At the moment, RapMap always prints unaligned reads, even if the -u flag is not given. The writeUnmapped variable seems to be set according to the flag, but is later...

ghost

mr-c

Figure out how to support a BSD or MIT license

3

Currently this is not possible as we rely on Jellyfish for the memory-efficient hash, parallel read parser, and basic k-mer operations. The read parser and (with some trouble) k-mer operations...

rob-p

Hi, I have pair-end reads from different organs and want to map them together to transcriptomes. Does RapMap support to map them together in one run? Bests, TF

xiaoyezao

mateIsFwd never gets a value set for unpaired hits

2

In RapMap v.0.5.0, the value of mateIsFwd is never set for unpaired hits in the function mergeLeftRightHits, in the file include/RapMapUtils.hpp. The function in question is below ``` inline void...

jenni-westoby

Hi, in the Debian packaging I formerly used the Debian packaged spdlog to avoid code copies as per Debian policy. Since spdlog in Debian switched to version 1.2 this does...

tillea

Hi, Do you have any experience in using the alignments produced by RapMap, perhaps with selective-alignment, for variant calling from RNA-seq? have you compared the results of variant calling with...

inti

I'm failing to compile release 0.5

4

I've got a several-year old installation of Arch, and I'm trying to compile RapMap to benchmark against some other aligners with in silico tests. I'm assessing accuracy and recall as...

darachm

I haven't been able to find a clear answer in the documentation: are the read counted as in all the transcripts they overlap or are they divided amongst them. If...

nachocab

Hi, the Debian package received a [bug report](https://bugs.debian.org/887943) about a failed build on the mips64el architecture. This might be a sign that the algorithm contains an issue that does not...

tillea