Closed zyhuang closed 1 year ago
Hi again,
I have a temporary fix for the issue above
diff --git a/phase_common/src/io/haplotype_writer.h b/phase_common/src/io/haplotype_writer.h
index ea0e3db..b0ad6fe 100644
--- a/phase_common/src/io/haplotype_writer.h
+++ b/phase_common/src/io/haplotype_writer.h
@@ -43,7 +43,7 @@ public:
~haplotype_writer();
//IO
- void writeHaplotypes(std::string foutput);
+ void writeHaplotypes(std::string foutput, double filter_maf);
};
#endif
diff --git a/phase_common/src/phaser/phaser_finalise.cpp b/phase_common/src/phaser/phaser_finalise.cpp
index f4fca41..fb0d2e9 100644
--- a/phase_common/src/phaser/phaser_finalise.cpp
+++ b/phase_common/src/phaser/phaser_finalise.cpp
@@ -38,7 +38,7 @@ void phaser::write_files_and_finalise() {
//step1: writing best guess haplotypes in VCF/BCF file
if (options.count("bingraph")) graph_writer(G, V).writeGraphs(options["bingraph"].as < std::string > ());
- if (options.count("output")) haplotype_writer(H, G, V, options["thread"].as < int > ()).writeHaplotypes(options["output"].as < std::string > (), options["filter-maf"].as < std::string > ());
+ if (options.count("output")) haplotype_writer(H, G, V, options["thread"].as < int > ()).writeHaplotypes(options["output"].as < std::string > (), options["filter-maf"].as < double > ());
//step2: Measure overall running time
vrb.bullet("Total running time = " + stb.str(tac.abs_time()) + " seconds");
Please see if this is useful or there are better ways. Thanks!
Best, Zhuoyi
Thanks for reporting this. I've just fixed it. Sorry about it, it's a development code that went into the main branch for some reasons...
Hello,
I noticed in a recent change in phase common module, it seems the method
haplotype_writer:: writeHaplotypes()
has inconsistent signature between the declaration and definition.https://github.com/odelaneau/shapeit5/blob/5680ff4ac9f726ba3445d24487fc024cc6f70c3e/phase_common/src/io/haplotype_writer.h#L46
https://github.com/odelaneau/shapeit5/blob/5680ff4ac9f726ba3445d24487fc024cc6f70c3e/phase_common/src/io/haplotype_writer.cpp#L39
This made it failed to build phase common tool.
The git version is
v1.0.0-beta-20-gacda0f5
.Maybe I missed something. Please let me know if there is a workaround for this. Thanks!
Best, Zhuoyi