bug fix in support for organisms with a different number of chromosomes

Author: omerwe

ldsc.py

@@ -603,6 +603,9 @@ def ldscore(args, log):
 parser.add_argument('--num-chr-sets', type=int, default=22,
     help='Number of chromosome sets for loco computations')
 
+parser.add_argument('--num-chr', type=int, default=22,
+    help='Number of chromosomes for the target organism (default is 22)')
+
 
 parser.add_argument('--no-standardize-ridge', default=False, action='store_true', 
     help='disable Ridge standardization')    

ldsc_polyfun/sumstats.py

@@ -248,6 +248,7 @@ def _merge_and_log(ld, sumstats, noun, log):
 
 
 def _read_ld_sumstats(args, log, fh, alleles=True, dropna=True):
+    _N_CHR = args.num_chr
     sumstats = _read_sumstats(args, log, fh, alleles=alleles, dropna=dropna)
     ref_ld = _read_ref_ld(args, log)
     n_annot = len(ref_ld.columns) - 2 #Changed to -2 because we also have chromosome column now