Pre-release v0.9.0

cpockrandt · Mar 11, 2021 · f4ca64d · f4ca64d
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diff --git a/README.rst b/README.rst
@@ -32,9 +32,9 @@ If you find our implementation useful and use it in your work, please consider c
 
 Please also consider citing the original method paper:
 
-    Lin MF, Jungreis I, and Kellis M. PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. Bioinformatics, 2011.
+    Lin MF et al. PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions. Bioinformatics, 2011.
 
-    Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright J, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary J, Frankish A, Kellis M (2019). Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Research gr-246462. doi: 10.1101/gr.246462.118.
+    Mudge JM et al. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci. Genome Research, 2019.
 
 .. _bioRxiv: https://doi.org/TODO
 

diff --git a/src/arg_parse.hpp b/src/arg_parse.hpp
@@ -469,6 +469,6 @@ class ArgParse {
     }
 };
 
-const std::string ArgParse::version = "v1.0.0";
+const std::string ArgParse::version = "v0.9.0";
 const std::string ArgParse::git_hash = xstr(GIT_HASH);
-const std::string ArgParse::git_date = xstr(GIT_DATE);
+const std::string ArgParse::git_date = xstr(GIT_DATE);
diff --git a/src/phylocsf++.cpp b/src/phylocsf++.cpp
@@ -22,7 +22,7 @@ int main(int argc, char **argv)
                   "For documentation and help, check out https://github.com/cpockrandt/PhyloCSFpp\n\n"
                   "Please consider citing:\n"
                   "  Pockrandt et al., PhyloCSF++: A fast and user-friendly implementation of PhyloCSF\n"
-                  "  with annotation tools, https://doi.org/10.1101/611160, bioRxiv 2021");
+                  "  with annotation tools, https://doi.org/TODO, bioRxiv 2021");
 
     args.add_subprogram("build-tracks", "Computes PhyloCSF and Power tracks for each codon and all 6 frames from alignments from MAF files. Outputs them in wig files.");
     args.add_subprogram("score-msa", "Computes PhyloCSF scores, ancestral sequence composition sores and branch length scores for entire alignments from MAF files. Outputs them in a BED-like format.");