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hsinnan75 / MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes
MIT License
30 stars 5 forks source link

Ability to use existing htslib ? #7

Closed tseemann closed 4 years ago

tseemann commented 4 years ago

It would be great if you could support linking against htslib I have installed already, rather than compiling your own version.

This would make it easier to package MapCaller into brew and bioconda.

Could you add a flag to the makefile, eg HTSLIB=/path/to/my/htslib ?

tseemann commented 4 years ago

I have tested this (I have libhts.so.2) and it works:

main:           $(OBJECT)
                        $(Compiler) $(FLAGS) $(OBJECT) -o MapCaller $(LIB) -lhts -lbz2 -llzma
hsinnan75 commented 4 years ago

I made some changes of htslib. Thus Mapcaller cannot use the original htslib. I'll try to fix this problem. Thank you.

tseemann commented 4 years ago

I compiled it with htslib 1.9 installed on my system.

What bugs will this cause?

hsinnan75 commented 4 years ago

htslib is used for outputing BAM file. However, I modified the original htslib source codes to change the arguments for the functions of SamHdr2BamHdr and sam_hdr_write. If you used a different version of htslib and would like to output the BAM file, MapCaller might fail to complete the task. I'll try to fix or remove this function from MapCaller in the future.

tseemann commented 4 years ago

Ok I will make sure not to use external htslib! Thank you