rqtl/qtl2: Version 0.22

Major changes Added some functions for diagnostics: recode_snps(), calc_raw_het(), calc_raw_geno_freq(), calc_raw_maf(), and calc_raw_founder_maf(). Added argument blup to fit1(), for getting BLUPs for a single fixed QTL position. At present, just gives estimates and coefficients by calling scan1blup() with a single position. pull_genoprobpos() can now take either a marker name (as before) or a set of map, chromosome, and position (from which it uses find_marker() to get the marker name). Added plot function for the results of compare_geno(). (Plots histogram of upper triangle.) Added functions n_founders() and founders() for getting the number of founders and the founder strain names for a cross2 object. scan1() now takes an optional hsq argument, so that the residual heritability may be specified rather than estimated. Minor changes write_control_file() now allows cross info codes with a cross info file (previously only allowed with a covariate). read_cross2() gives a warning if there are cross info conversion codes but more than one cross info column. Small fix in read_cross2() to allow multiple cross info covariates. Added a check that the founder genotypes have the same strain IDs on each chromosome. convert2cross2() now includes alleles component even if it wasn't present as an attribute. Added function sdp2char() for converting numeric SDP codes to character strings like "ABC|DEFGH". Updated mouse gene database with 2019-08-12 data from MGI. get_common_ids() strips off names from output, just in case. Added internal functions rqtl1_crosstype() and rqtl1_chrtype(). Bug fixes Fixed typo in help for scan1() and related functions. genoprob_to_snpprob() was giving an error if you gave a cross2 object in place of a snpinfo table and it had monomorphic markers. Fixed problem with weights in scan1() and related functions when their derived from table(). Make sure they're a plain numeric vector, not an array. Fixed check_cross2(): the check for invalid genotypes wasn't happening. Better error message for the case that there are no markers in common between map and genotypes. extract_dim_from_header(), used by read_cross2() and read_csv(), now just looks for the number part in the rest of the line. maxlod() now handles missing values (forcing na.rm=TRUE). If all values are missing it gives a warning and returns -Inf. [Fixes Issue #134.] In max_scan1(), treat the case that the input has no column names. [Fixes Issue #133.] max_scan1() was giving a messed up error message if lodcolumn was out of range. [Fixes Issue #132.] Revised the script inst/scripts/create_ccvariants.R to capture all of the consequences and genes for each SNP (rather than just the first), and fixing a bug that prevented capture of indels from chromosomes 6-X. Consequently, revised the example SQLite database extdata/cc_variants_small.sqlite and associated tests