GraphAligner closes named pipe (feature request)

[nrizzo]

Hello!

GraphAligner is not nice to Unix named pipes for the input reads (see below). I think named pipe compatibility could be useful in pipelines that feed GraphAligner the reads and do not want to store them on disk, would you consider adding a flag parameter about it?

# shell 0
$ mkfifo test/fiforead.fa
$ cat test/read.fa > test/fiforead.fa
$ echo $?
141

# shell 1
$ GraphAligner -g test/graph.gfa -f test/fiforead.fa -a test/aln.gaf -x vg
GraphAligner Branch master commit daec67f67a2f50d648a6aa30cbbe5a2949583061 2024-01-19 10:52:13 +0200
GraphAligner Branch master commit daec67f67a2f50d648a6aa30cbbe5a2949583061 2024-01-19 10:52:13 +0200
Load graph from test/graph.gfa
Build alignment graph
Build minimizer seeder from the graph
Minimizer seeds, length 15, window size 20, density 10
Seed cluster size 1
Extend up to 5 seed clusters
Alignment bandwidth 10
Clip alignment ends with identity < 66%
X-drop DP score cutoff 14705
Backtrace from 10 highest scoring local maxima per cluster
write alignments to test/aln.gaf
Align
# I guess here SIGPIPE happens in shell 0

Execution proceeds as normal if I rerun command cat test/read.fa > test/fiforead.fa in the first shell, and I can't seem to replicate a run where this would not align any read (huh, maybe with fastq?). Culprits are the lines src/Aligner.cpp:810-818 opening and closing the read file, commenting out those lines fixes the problem.

Let me know if you want me to attempt the fork, patch, and pull-request. Thanks! ~Nicola

[caineblood]

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