Dylan Aïssi pushed to branch master at Debian Med / plink1.9
Commits: 179bb503 by Dylan Aïssi at 2018-03-08T21:45:50+01:00 New upstream version 1.90~b5.3-180221 - - - - - a142d833 by Dylan Aïssi at 2018-03-08T21:45:54+01:00 Merge tag 'upstream/1.90_b5.3-180221' Upstream version 1.90~b5.3-180221 - - - - - 2dae8eb5 by Dylan Aïssi at 2018-03-08T21:55:40+01:00 Update changelogs - - - - - caee70d9 by Dylan Aïssi at 2018-03-08T22:01:44+01:00 Upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - debian/upstream.docs/upstream.changelog - plink.c - plink_data.c Changes: ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +plink1.9 (1.90~b5.3-180221-1) unstable; urgency=medium + + * New upstream release. + + -- Dylan Aïssi <[email protected]> Thu, 08 Mar 2018 21:50:36 +0100 + plink1.9 (1.90~b5.2-180109-1) unstable; urgency=medium * New upstream release. ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Dylan Aïssi <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11), +Build-Depends: debhelper (>= 11~), help2man, libatlas-base-dev, liblapack-dev, ===================================== debian/upstream.docs/upstream.changelog ===================================== --- a/debian/upstream.docs/upstream.changelog +++ b/debian/upstream.docs/upstream.changelog @@ -1,5 +1,7 @@ # Copy/Paste from https://www.cog-genomics.org/plink/1.9/ +21 Feb 2018: "--indiv-sort file" no longer scrambles the phenotypes when used with --{b}merge or --merge-list. + 9 Jan 2018: --all-pheno no longer gets into an infinite loop when one phenotype is all-missing. 20 Dec 2017: --meta-analysis 'report-all' now reports original stats instead of 'NA' when N=1. Fixed an inaccuracy in --adjust's handling of very small p-values. --make-just-fam works properly with just .fam input again. ===================================== plink.c ===================================== --- a/plink.c +++ b/plink.c @@ -93,7 +93,7 @@ static const char ver_str[] = #ifdef STABLE_BUILD - "PLINK v1.90b5.2" + "PLINK v1.90b5.3" #else "PLINK v1.90p" #endif @@ -105,10 +105,10 @@ static const char ver_str[] = #else " 32-bit" #endif - " (9 Jan 2018)"; + " (21 Feb 2018)"; static const char ver_str2[] = // include leading space if day < 10, so character length stays the same - " " + "" #ifdef STABLE_BUILD " " // (don't want this when version number has two trailing digits) #else ===================================== plink_data.c ===================================== --- a/plink_data.c +++ b/plink_data.c @@ -16203,11 +16203,11 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam } if (is_dichot_pheno) { if (qsort_ext(sample_fids, tot_sample_ct, max_sample_full_len, merge_nsort? strcmp_natural_deref : strcmp_deref, pheno_c_char, 1)) { - goto merge_datasets_ret_NOMEM; + goto merge_datasets_ret_NOMEM; } } else { if (qsort_ext(sample_fids, tot_sample_ct, max_sample_full_len, merge_nsort? strcmp_natural_deref : strcmp_deref, (char*)pheno_d, sizeof(double))) { - goto merge_datasets_ret_NOMEM; + goto merge_datasets_ret_NOMEM; } } if (sample_sort == SAMPLE_SORT_FILE) { @@ -16284,10 +16284,12 @@ int32_t merge_datasets(char* bedname, char* bimname, char* famname, char* outnam goto merge_datasets_ret_WRITE_FAIL; } if (is_dichot_pheno) { - cc = pheno_c_char[ulii]; + // bugfix (21 Feb 2018): need to use the map_reverse index here, + // since the phenotypes correspond to ASCII-sorted sample ID order. + cc = pheno_c_char[ujj]; fprintf(outfile, "\t%s\n", cc? ((cc == 1)? "2" : "-9") : "1"); } else { - fprintf(outfile, "\t%g\n", pheno_d[ulii]); + fprintf(outfile, "\t%g\n", pheno_d[ujj]); } } } View it on GitLab: https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c --- View it on GitLab: https://salsa.debian.org/med-team/plink1-9/compare/bd4222a7a1bf21c2c09b75090b6934ec353dca84...caee70d9c7dbb4182e258c36526a41ec825f742c You're receiving this email because of your account on salsa.debian.org.
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