User: Click downvote
Click downvote • 670
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... Thanks, will start to read up on it. ...
written 4 months ago by
Click downvote • 670
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... 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 4 months ago by
Click downvote • 670
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... Getting the start, len, strand and reference. It is for a ChIP-Seq caller :) ...
written 4 months ago by
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5 follow
1
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... 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 ...
written 5 months ago by
Click downvote • 670
• updated
4 months ago by
John Marshall • 1.5k
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... 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 5 months ago by
Click downvote • 670
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... 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 5 months ago by
Click downvote • 670
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... 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 5 months ago by
Click downvote • 670
2
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... I will submit to all of your expertise. Added htslib in a lib folder in my project. ...
written 5 months ago by
Click downvote • 670
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267
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... But pysam is slow as each record is a Python object which needs to be parsed. ...
written 5 months ago by
Click downvote • 670
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267
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... 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 5 months ago by
Click downvote • 670
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