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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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compile error with CNVnator 0.4.1 #173

Closed mwaldron104 closed 5 years ago

mwaldron104 commented 5 years ago

I downloaded and compiled latest samtools (1.9), but I'm getting what looks like a samtools-related error when compiling CNVnator:

$ ▶ make Compiling with parallel (OpenMP) support g++ -O3 -std=c++11 -DCNVNATOR_VERSION=\"v0.4.1\" -fopenmp -I/usr/include/root -Isamtools -c cnvnator.cpp -o obj/cnvnator.o In file included from cnvnator.cpp:14:0: AliParser.hh:18:3: error: ‘samfile_t’ does not name a type samfile_t file; ^ AliParser.hh:19:3: error: ‘bam_index_t’ does not name a type bam_index_t index; ^ AliParser.hh: In member function ‘std::string AliParser::getQueryName()’: AliParser.hh:98:69: error: ‘bam1_qname’ was not declared in this scope inline string getQueryName() { return (record) ? bam1_qname(record) : ""; } ^ make: *** [obj/cnvnator.o] Error 1

mwaldron104 commented 5 years ago

I was able to resolve this by making some edits to the Makefile, so that it could properly find my samtools, htslib and root files.

lunalvan commented 1 year ago

Hi! I am having the same issue when trying to install CNVnator. Do you by any chance know what edits you made to the Makefile?

ChengQin0 commented 1 year ago

+1

abyzov commented 1 year ago

Please consider switching to CNVpytor https://github.com/abyzovlab/cnvpytor Thanks.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic

Mayo Clinic, 200 1st street SW, Harwick 7-91 Rochester, MN 55905 www.abyzovlab.org http://www.abyzovlab.orgtel: +1-(507)-538-0978