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User: Click downvote

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Posts by Click downvote

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Comment: C: Minimal example of using htslib from conda to build a simple c file?
... Thanks, will start to read up on it. ...
written 2.2 years ago by Click downvote • 690
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Comment: C: Minimal example of using htslib from conda to build a simple c file?
... It is a reimplementation of a very popular piece of software. It is already working well, I am just irked that reading bam takes 3x as long as bed reading. ...
written 2.2 years ago by Click downvote • 690
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Comment: C: Minimal example of using htslib from conda to build a simple c file?
... Getting the start, len, strand and reference. It is for a ChIP-Seq caller :) ...
written 2.2 years ago by Click downvote • 690
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Minimal example of using htslib from conda to build a simple c file?
... This is a tiny script that is enough to get gcc to fail when trying to build: #include #include #include #include int main(int argc, char *argv[]){ samFile *fp_in = hts_open(argv[1],"r"); //open bam file bam_hdr_t *bamHdr = sam_hdr_read(fp_in); //re ...
C conda htslib written 2.2 years ago by Click downvote • 690 • updated 2.2 years ago by John Marshall ♦ 2.2k
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Comment: C: Is there a single header file somewhere I can use to read bam?
... I just need to stream the file. I guess the error is on my part as I have not used C much, just Cython. ...
written 2.2 years ago by Click downvote • 690
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Comment: C: Is there a single header file somewhere I can use to read bam?
... But I have the htslib conda installed and still #include errors. I think I will just use pysam, but give a warning that it is slower than the C++ bed reader. ...
written 2.2 years ago by Click downvote • 690
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Comment: C: Is there a single header file somewhere I can use to read bam?
... But I am using cython. How can I use compile flags to point to the system installation of htslib? Users have no way to point to an installed version when `pip installing` my library. ...
written 2.2 years ago by Click downvote • 690
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Answer: C: Is there a single header file somewhere I can use to read bam?
... I will submit to all of your expertise. Added htslib in a lib folder in my project. ...
written 2.2 years ago by Click downvote • 690
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Comment: C: Is there a single header file somewhere I can use to read bam?
... But pysam is slow as each record is a Python object which needs to be parsed. ...
written 2.2 years ago by Click downvote • 690
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Comment: A: Is there a single header file somewhere I can use to read bam?
... MACS2 seems to be able to read bam without any special utilities: https://github.com/taoliu/MACS/blob/33187eae605081c8ddad9313a886bd01d2c654cd/MACS2/IO/Parser.pyx#L732 However, I do not know if the code is brittle, or especially fast. It used the struct library so it cannot be compiled down to pure ...
written 2.2 years ago by Click downvote • 690

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