fix --ld-snps

chrchang · Jan 13, 2017 · 87da0eb · 87da0eb
1 parent 6b05d89
commit 87da0eb
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Showing 39 changed files with 47 additions and 43 deletions.
diff --git a/plink.c b/plink.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify
@@ -93,7 +93,7 @@
 
 static const char ver_str[] =
 #ifdef STABLE_BUILD
-  "PLINK v1.90b3.44"
+  "PLINK v1.90b3.45"
 #else
   "PLINK v1.90p"
 #endif
@@ -105,7 +105,7 @@ static const char ver_str[] =
 #else
   " 32-bit"
 #endif
-  " (27 Dec 2016)";
+  " (13 Jan 2017)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""
@@ -118,7 +118,7 @@ static const char ver_str2[] =
   "  "
 #endif
   "    https://www.cog-genomics.org/plink2\n"
-  "(C) 2005-2016 Shaun Purcell, Christopher Chang   GNU General Public License v3"
+  "(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3"
 #if SPECIES_DEFAULT > 0
   "\nRecompiled with default species = "
   #if SPECIES_DEFAULT == SPECIES_COW

diff --git a/plink_assoc.c b/plink_assoc.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_assoc.h b/plink_assoc.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_ASSOC_H__
 #define __PLINK_ASSOC_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_calc.c b/plink_calc.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_cluster.c b/plink_cluster.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_cnv.c b/plink_cnv.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_cnv.h b/plink_cnv.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_CNV_H__
 #define __PLINK_CNV_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_common.c b/plink_common.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_common.h b/plink_common.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_COMMON_H__
 #define __PLINK_COMMON_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_data.c b/plink_data.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_data.h b/plink_data.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_DATA_H__
 #define __PLINK_DATA_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_dosage.c b/plink_dosage.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_dosage.h b/plink_dosage.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_DOSAGE_H__
 #define __PLINK_DOSAGE_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_family.c b/plink_family.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_family.h b/plink_family.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_FAMILY_H__
 #define __PLINK_FAMILY_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_filter.c b/plink_filter.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_filter.h b/plink_filter.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_FILTER_H__
 #define __PLINK_FILTER_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_glm.c b/plink_glm.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_glm.h b/plink_glm.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_GLM_H__
 #define __PLINK_GLM_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_help.c b/plink_help.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_help.h b/plink_help.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_HELP_H__
 #define __PLINK_HELP_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_homozyg.c b/plink_homozyg.c
@@ -1,5 +1,5 @@
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_homozyg.h b/plink_homozyg.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_HOMOZYG_H__
 #define __PLINK_HOMOZYG_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_lasso.c b/plink_lasso.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_lasso.h b/plink_lasso.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_LASSO_H__
 #define __PLINK_LASSO_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_ld.c b/plink_ld.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify
@@ -5799,8 +5799,12 @@ int32_t ld_report_regular(pthread_t* threads, Ld_info* ldip, FILE* bedfile, uint
 	}
       } else {
         retval = string_range_list_to_bitarr2(sorted_ids, id_map, marker_ct, max_marker_id_len, &(ldip->snps_rl), "ld-snps", marker_exclude_idx1);
+	if (retval) {
+	  goto ld_report_regular_ret_1;
+	}
         bitvec_or(marker_exclude, unfiltered_marker_ctl, marker_exclude_idx1);
-        marker_ct1 = marker_ct - popcount_longs(marker_exclude_idx1, unfiltered_marker_ctl);
+	// bugfix, 13 Jan 2017
+        marker_ct1 = unfiltered_marker_ct - popcount_longs(marker_exclude, unfiltered_marker_ctl);
       }
       if (!marker_ct1) {
 	goto ld_report_regular_ret_EMPTY_SET1;

diff --git a/plink_ld.h b/plink_ld.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_LD_H__
 #define __PLINK_LD_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_matrix.c b/plink_matrix.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_matrix.h b/plink_matrix.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_MATRIX_H__
 #define __PLINK_MATRIX_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_misc.c b/plink_misc.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_misc.h b/plink_misc.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_MISC_H__
 #define __PLINK_MISC_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_perm.c b/plink_perm.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_perm.h b/plink_perm.h
@@ -1,6 +1,6 @@
 #ifndef __PLINK_PERM_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_rserve.c b/plink_rserve.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_rserve.h b/plink_rserve.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_RSERVE_H__
 #define __PLINK_RSERVE_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_set.c b/plink_set.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_set.h b/plink_set.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_SET_H__
 #define __PLINK_SET_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_stats.c b/plink_stats.c
@@ -1,4 +1,4 @@
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify

diff --git a/plink_stats.h b/plink_stats.h
@@ -1,7 +1,7 @@
 #ifndef __PLINK_STATS_H__
 #define __PLINK_STATS_H__
 
-// This file is part of PLINK 1.90, copyright (C) 2005-2016 Shaun Purcell,
+// This file is part of PLINK 1.90, copyright (C) 2005-2017 Shaun Purcell,
 // Christopher Chang.
 //
 // This program is free software: you can redistribute it and/or modify