Erik Garrison

thread safety

22

I'm learning through trial and error that not all classes in sdsl-lite are thread safe ([for instance](https://github.com/simongog/sdsl-lite/issues/235)). Is there documentation about what features of sdsl-lite are thread safe? I have...

make wt_int and wm_int thread safe

12

This is accomplished by moving m_path_off and m_path_rank_off to the local context of select (see #263). Now, grep mutable include/sdsl/*hpp yields only wt_pc.hpp, bp_support_sada, and csa_sada, all of which have...

graph subsetting operations and serialization format

29

I'd like to query a part of the graph using coordinates against an arbitrary reference path encoded in it. I have a implementation of this kind of feature that can...

Where are sequences stored in the graph?

14

Reading [common.avdl](https://github.com/ga4gh/schemas/blob/master/src/main/resources/avro/common.avdl#L8), I'm curious where the association between actual DNA sequences and segments is made. Why should it not be possible to directly access the sequences associated with a particular...

This implements updates that allow us to run mashmap-align in parallel. The technique is to read candidate alignments into an atomic queue, from which worker threads pick them up, writing...

encourage dataflow programmers to switch to streem from shell

4

I do a lot of flow-oriented programming in shell, so I'm interested in streem as a replacement for the traditional unix shell. (I use zsh, but the differences are minimal...

CMakeify

8

This adds CMakeLists.txt to make it easier to build a static library from lodepng and also the examples. I don't compile all of them. I'm worried that the dependency on...

GFA output

15

Have you considered adding GFA output to abPOA? I am likely to make a patch to do this, but I wouldn't mind if you beat me to it. 🙂

[simd_abpoa_align_sequence_to_subgraph1] Error in cg_backtrack. (4)

17

I finally found a small reproducible example of an alignment problem. To reproduce on this input FASTA, [fail_smoothxg_block_3055.fa.txt](https://github.com/yangao07/abPOA/files/5334048/fail_smoothxg_block_3055.fa.txt): ``` abpoa -s -r 3 fail_smoothxg_block_3055.fa [simd_abpoa_align_sequence_to_subgraph1] Error in cg_backtrack. (4) ```

Tests

2

Do you have test scripts for bgt?