Comments (2)
You are exactly right. This is an unintended consequence of sub-optimal implementation of some old subroutines. From my perspective, it is not a priority to optimize input from a pipe, saving to a temporary file is a reasonable work-around.
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I understand. If, on our end, we feel that it is important to support pipe input, we will submit a pull request. One possibly interesting use case is online mapping. In this mode of operation, new map requests can be submitted on-the-fly to a long-lived or persistent urmap process (just by feeding it another input record), amortizing the startup cost and providing real-time and parallelized map responses. With the pipe input fixes (*), this seems to work pretty well. I believe this mode of operation may represent a significant upgrade to urmap's capabilities, and cannot be supported via the workaround you described.
(*) along with some modifications to the line reading code, basically just replacing it with fgets instead of using custom buffering
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Related Issues (9)
- Complie error and solution on RHEL 6
- Segfault if read length is < index word length
- Bad fastq file HOT 1
- Possible to output NM aux tag? HOT 3
- Compile error at myutils.cpp:1403:27 HOT 5
- MD:Z tag for calculate identity and interleaved reads
- Multithreading HOT 16
- bug in ExtendPen (invalid memory access, reading past the end of DBSeq)
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