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bob.dybian-guest pushed a commit to branch master
in repository plink1.9.
commit ae340cc2bfb39d6e618f37634f3c8db92929e716
Author: Dylan Aïssi <bob.dyb...@gmail.com>
Date: Tue Sep 12 10:17:16 2017 +0200
New upstream version 1.90~b4.7-170906
---
Makefile | 63 +++++++++++++++++++++----------
plink.c | 69 ++++++++++++++++++++++++----------
plink_calc.c | 6 +--
plink_common.c | 2 +-
plink_data.c | 27 +++++++++-----
plink_data.h | 2 +
plink_help.c | 8 ++--
plink_lasso.c | 115 ++++++++++++++++++++++++++++-----------------------------
plink_lasso.h | 4 +-
plink_rserve.c | 7 +++-
plink_rserve.h | 2 +-
11 files changed, 184 insertions(+), 121 deletions(-)
diff --git a/Makefile b/Makefile
index 7b45e20..7e1c335 100644
--- a/Makefile
+++ b/Makefile
@@ -8,10 +8,10 @@
NO_LAPACK =
# Variable that allows additional linker flags (e.g., "-L/path/to/libs") to be
-# passed into the linker; to use this, invoke 'make LINKFLAGS_EXTRA="<opts>"'.
-LINKFLAGS_EXTRA =
+# passed into the linker; to use this, invoke 'make LDFLAGS_EXTRA="<opts>"'.
+LDFLAGS_EXTRA =
-.PHONY: clean
+.PHONY: clean install
# should autodetect system
SYS = UNIX
@@ -24,19 +24,30 @@ else
endif
endif
-CFLAGS=-Wall -O2
-BLASFLAGS=-L/usr/lib64/atlas -llapack -lcblas -latlas
-LINKFLAGS=-lm -lpthread -ldl
-ZLIB=../zlib-1.2.11/libz.so.1.2.11
+# Allow these to be overridden by make arguments or env variables, so people
+# don't have to edit the Makefile to build in a different environment.
+BIN ?= plink
+CC ?= gcc
+CXX ?= g++
+CFLAGS ?= -Wall -O2
+CXXFLAGS ?= -Wall -O2
+BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lcblas -latlas
+LDFLAGS ?= -lm -lpthread -ldl
+ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11
+
+PREFIX ?= /usr/local
+DESTDIR ?= .
+INSTALL ?= install
+STRIP ?= strip
ifeq ($(SYS), MAC)
GCC_GTEQ_43 := $(shell expr `g++ -dumpversion | sed -e
's/\.\([0-9][0-9]\)/\1/g' -e 's/\.\([0-9]\)/0\1/g' -e 's/^[0-9]\{3,4\}$$/&00/'`
\>= 40300)
ifeq "$(GCC_GTEQ_43)" "1"
- CFLAGS=-Wall -O2 -flax-vector-conversions
+ CFLAGS ?= -Wall -O2 -flax-vector-conversions
endif
- BLASFLAGS=-framework Accelerate
- LINKFLAGS=-ldl
- ZLIB=../zlib-1.2.11/libz.1.2.11.dylib
+ BLASFLAGS ?= -framework Accelerate
+ LDFLAGS ?= -ldl
+ ZLIB ?= ../zlib-1.2.11/libz.1.2.11.dylib
endif
ifeq ($(SYS), WIN)
@@ -45,9 +56,9 @@ ifeq ($(SYS), WIN)
# on Windows.
# If you don't already have LAPACK built, you'll probably want to turn on
# NO_LAPACK.
- BLASFLAGS=-L. lapack/liblapack.a -L. lapack/librefblas.a
- LINKFLAGS=-lm -static-libgcc
- ZLIB=../zlib-1.2.11/libz.a
+ BLASFLAGS ?= -L. lapack/liblapack.a -L. lapack/librefblas.a
+ LDFLAGS ?= -lm -static-libgcc
+ ZLIB ?= ../zlib-1.2.11/libz.a
endif
ifdef NO_LAPACK
@@ -57,23 +68,35 @@ endif
OBJS = plink.o plink_assoc.o plink_calc.o plink_cluster.o plink_cnv.o
plink_common.o plink_data.o plink_dosage.o plink_family.o plink_filter.o
plink_glm.o plink_help.o plink_homozyg.o plink_lasso.o plink_ld.o
plink_matrix.o plink_misc.o plink_perm.o plink_rserve.o plink_set.o
plink_stats.o SFMT.o dcdflib.o pigz.o yarn.o Rconnection.o hfile.o bgzf.o
# In the event that you are still concurrently using PLINK 1.07, we suggest
-# renaming that binary to "plink107", and this one to "plink1".
+# renaming that binary to "plink107", and this one to "plink" or "plink1".
+
+all: $(BIN)
plink: $(OBJS)
- g++ $^ $(LINKFLAGS_EXTRA) $(BLASFLAGS) $(LINKFLAGS) -L. $(ZLIB) -o $@
+ $(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o
$@
plinkw: $(OBJS)
- gfortran -O2 $^ $(LINKFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS)
$(LINKFLAGS) -L. $(ZLIB) -o $@
+ gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS)
$(LDFLAGS) -L. $(ZLIB) -o $@
+
+install:
+ $(INSTALL) -d $(DESTDIR)$(PREFIX)/bin
+ $(INSTALL) -c $(BIN) $(DESTDIR)$(PREFIX)/bin
+
+install-strip: install
+ $(STRIP) $(DESTDIR)$(PREFIX)/bin/$(BIN)
clean:
rm -f $(OBJS) plink plinkw
-
# Pattern-based rules for compiling object (.o) files; basically identical to
# GNU make's built-in rules, except we explicitly use "g++" instead of $(CC).
+# Compiling C files with a C++ compiler is deprecated, but the code needs
+# to be cleaned up before we can switch to cc. E.g. plink_rserve.c
+# includes a C++ header and exposed functions will need to be declared with
+# extern "C".
%.o: %.c
- g++ -c $(CFLAGS) $< -o $@
+ $(CXX) -c $(CFLAGS) $< -o $@
%.o: %.cc
- g++ -x c++ -c $(CFLAGS) $< -o $@
+ $(CXX) -x c++ -c $(CXXFLAGS) $< -o $@
diff --git a/plink.c b/plink.c
index 4e3d37c..3f707ed 100644
--- a/plink.c
+++ b/plink.c
@@ -93,7 +93,7 @@
static const char ver_str[] =
#ifdef STABLE_BUILD
- "PLINK v1.90b4.4"
+ "PLINK v1.90b4.7"
#else
"PLINK v1.90p"
#endif
@@ -105,10 +105,10 @@ static const char ver_str[] =
#else
" 32-bit"
#endif
- " (31 May 2017)";
+ " (6 Sep 2017)";
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 a trailing letter)
#else
@@ -319,7 +319,7 @@ static inline int32_t relationship_or_ibc_req(uint64_t
calculation_type) {
return (relationship_req(calculation_type) || (calculation_type & CALC_IBC));
}
-int32_t plink(char* outname, char* outname_end, char* bedname, char* bimname,
char* famname, char* cm_map_fname, char* cm_map_chrname, char* phenoname, char*
extractname, char* excludename, char* keepname, char* removename, char*
keepfamname, char* removefamname, char* filtername, char* freqname, char*
distance_wts_fname, char* read_dists_fname, char* read_dists_id_fname, char*
evecname, char* mergename1, char* mergename2, char* mergename3, char*
missing_mid_template, char* missing_marke [...]
+int32_t plink(char* outname, char* outname_end, char* bedname, char* bimname,
char* famname, char* cm_map_fname, char* cm_map_chrname, char* phenoname, char*
extractname, char* excludename, char* keepname, char* removename, char*
keepfamname, char* removefamname, char* filtername, char* freqname, char*
distance_wts_fname, char* read_dists_fname, char* read_dists_id_fname, char*
evecname, char* mergename1, char* mergename2, char* mergename3, char*
missing_mid_template, char* missing_marke [...]
FILE* bedfile = nullptr;
FILE* phenofile = nullptr;
uintptr_t unfiltered_marker_ct = 0;
@@ -479,16 +479,7 @@ int32_t plink(char* outname, char* outname_end, char*
bedname, char* bimname, ch
goto plink_ret_OPEN_FAIL;
}
memcpy(outname_end, ".bed", 5);
- // if file doesn't exist, realpath returns nullptr on Linux instead of what
- // the path would be.
-#ifdef _WIN32
- uii = GetFullPathName(outname, FNAMESIZE, &(g_textbuf[FNAMESIZE + 64]),
nullptr);
- if (uii && (uii <= FNAMESIZE) && (!strcmp(g_textbuf, &(g_textbuf[FNAMESIZE
+ 64]))))
-#else
- cptr = realpath(outname, &(g_textbuf[FNAMESIZE + 64]));
- if (cptr && (!strcmp(g_textbuf, &(g_textbuf[FNAMESIZE + 64]))))
-#endif
- {
+ if (realpath_identical(outname, g_textbuf, &(g_textbuf[FNAMESIZE + 64]))) {
logprint("Note: --make-bed input and output filenames match. Appending
'~' to input\nfilenames.\n");
uii = strlen(bedname);
memcpy(g_textbuf, bedname, uii + 1);
@@ -1919,7 +1910,7 @@ int32_t plink(char* outname, char* outname_end, char*
bedname, char* bimname, ch
#if defined __cplusplus && !defined _WIN32
if (calculation_type & CALC_RPLUGIN) {
- retval = rserve_call(rplugin_fname, rplugin_port, (misc_flags /
MISC_RPLUGIN_DEBUG) & 1, bedfile, bed_offset, marker_ct, unfiltered_marker_ct,
marker_exclude, marker_reverse, marker_ids, max_marker_id_len,
marker_allele_ptrs, marker_pos, plink_maxsnp, chrom_info_ptr,
unfiltered_sample_ct, pheno_nm, pheno_nm_ct, pheno_c, pheno_d, cluster_ct,
cluster_map, cluster_starts, covar_ct, covar_d, outname, outname_end);
+ retval = rserve_call(rplugin_fname, rplugin_host_or_socket, rplugin_port,
(misc_flags / MISC_RPLUGIN_DEBUG) & 1, bedfile, bed_offset, marker_ct,
unfiltered_marker_ct, marker_exclude, marker_reverse, marker_ids,
max_marker_id_len, marker_allele_ptrs, marker_pos, plink_maxsnp,
chrom_info_ptr, unfiltered_sample_ct, pheno_nm, pheno_nm_ct, pheno_c, pheno_d,
cluster_ct, cluster_map, cluster_starts, covar_ct, covar_d, outname,
outname_end);
if (retval) {
goto plink_ret_1;
}
@@ -1927,7 +1918,7 @@ int32_t plink(char* outname, char* outname_end, char*
bedname, char* bimname, ch
#endif
if (calculation_type & CALC_LASSO_LAMBDA) {
- retval = lasso_lambda(marker_exclude, marker_reverse, chrom_info_ptr,
sex_male, pheno_nm, covar_nm, bed_offset, unfiltered_marker_ct, marker_ct,
unfiltered_sample_ct, pheno_nm_ct, hh_exists, lasso_lambda_iters, lasso_h2,
bedfile, outname, outname_end, &lasso_minlambda);
+ retval = lasso_lambda(marker_exclude, marker_reverse, chrom_info_ptr,
sample_exclude, sex_male, pheno_nm, covar_nm, bed_offset, unfiltered_marker_ct,
marker_ct, unfiltered_sample_ct, sample_ct, pheno_nm_ct, hh_exists,
lasso_lambda_iters, lasso_h2, bedfile, outname, outname_end, &lasso_minlambda);
if (retval) {
goto plink_ret_1;
}
@@ -2086,7 +2077,7 @@ int32_t plink(char* outname, char* outname_end, char*
bedname, char* bimname, ch
}
}
if (calculation_type & CALC_LASSO) {
- retval = lasso(threads, bedfile, bed_offset, outname, outname_end2,
unfiltered_marker_ct, marker_exclude, marker_ct, marker_ids, max_marker_id_len,
marker_allele_ptrs, marker_reverse, chrom_info_ptr, unfiltered_sample_ct,
pheno_nm_ct, lasso_h2, lasso_minlambda, lasso_select_covars_range_list_ptr,
misc_flags, pheno_nm, pheno_c, pheno_d, covar_ct, covar_names,
max_covar_name_len, covar_nm, covar_d, sex_male, hh_exists);
+ retval = lasso(threads, bedfile, bed_offset, outname, outname_end2,
unfiltered_marker_ct, marker_exclude, marker_ct, marker_ids, max_marker_id_len,
marker_allele_ptrs, marker_reverse, chrom_info_ptr, unfiltered_sample_ct,
sample_ct, pheno_nm_ct, lasso_h2, lasso_minlambda,
lasso_select_covars_range_list_ptr, misc_flags, sample_exclude, pheno_nm,
pheno_c, pheno_d, covar_ct, covar_names, max_covar_name_len, covar_nm, covar_d,
sex_male, hh_exists);
if (retval) {
goto plink_ret_1;
}
@@ -3181,9 +3172,10 @@ int32_t main(int32_t argc, char** argv) {
char* metaanal_pfield_search_order = nullptr;
char* metaanal_essfield_search_order = nullptr;
char* rplugin_fname = nullptr;
+ char* rplugin_host_or_socket = nullptr;
uint32_t gene_report_border = 0;
uint32_t metaanal_flags = 0;
- uint32_t rplugin_port = 6311;
+ int32_t rplugin_port = -2; // now interpreted by rserve_call() as default
double vcf_min_qual = -1;
double vcf_min_gq = -1;
double vcf_min_gp = -1;
@@ -4177,7 +4169,7 @@ int32_t main(int32_t argc, char** argv) {
if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
goto main_ret_INVALID_CMDLINE_2A;
}
- if (scan_posint_capped(argv[cur_arg + 1], 65535, &rplugin_port)) {
+ if (scan_posint_capped(argv[cur_arg + 1], 65535,
(uint32_t*)(&rplugin_port))) {
sprintf(g_logbuf, "Error: Invalid --R-port parameter '%s'.\n",
argv[cur_arg + 1]);
goto main_ret_INVALID_CMDLINE_WWA;
}
@@ -4189,6 +4181,39 @@ int32_t main(int32_t argc, char** argv) {
logprint("Note: --R-debug flag deprecated. Use e.g. '--R [filename]
debug'.\n");
misc_flags |= MISC_RPLUGIN_DEBUG;
goto main_param_zero;
+ } else if (!memcmp(argptr2, "-host", 6)) {
+ if (!rplugin_fname) {
+ logerrprint("Error: --R-host must be used with --R.\n");
+ goto main_ret_INVALID_CMDLINE;
+ }
+ if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
+ goto main_ret_INVALID_CMDLINE_2A;
+ }
+ retval = alloc_string(&rplugin_host_or_socket, argv[cur_arg + 1]);
+ if (retval) {
+ goto main_ret_INVALID_CMDLINE_WWA;
+ }
+ } else if (!memcmp(argptr2, "-socket", 8)) {
+ if (!rplugin_fname) {
+ logerrprint("Error: --R-socket must be used with --R.\n");
+ goto main_ret_INVALID_CMDLINE;
+ }
+ if (rplugin_port != -2) {
+ logerrprint("Error: --R-socket cannot be used with --R-port.\n");
+ goto main_ret_INVALID_CMDLINE;
+ }
+ if (rplugin_host_or_socket) {
+ logerrprint("Error: --R-socket cannot be used with --R-host.\n");
+ goto main_ret_INVALID_CMDLINE;
+ }
+ if (enforce_param_ct_range(param_ct, argv[cur_arg], 1, 1)) {
+ goto main_ret_INVALID_CMDLINE_2A;
+ }
+ retval = alloc_string(&rplugin_host_or_socket, argv[cur_arg + 1]);
+ if (retval) {
+ goto main_ret_INVALID_CMDLINE_WWA;
+ }
+ rplugin_port = -1;
} else {
goto main_ret_INVALID_CMDLINE_UNRECOGNIZED;
}
@@ -7530,6 +7555,9 @@ int32_t main(int32_t argc, char** argv) {
sprintf(g_logbuf, "Error: Invalid increment '%s' for --%s.\n",
argv[cur_arg + param_ct - 1], argptr);
goto main_ret_INVALID_CMDLINE_WWA;
}
+ if ((ld_info.modifier & LD_PRUNE_KB_WINDOW) &&
(ld_info.prune_window_incr > 1)) {
+ LOGERRPRINTFWW("Warning: --%s step size should be 1 when window size
is in kb units.\n", argptr);
+ }
if (scan_double(argv[cur_arg + param_ct], &ld_info.prune_last_param) ||
(ld_info.prune_last_param < 0.0) || (ld_info.prune_last_param >= 1.0)) {
sprintf(g_logbuf, "Error: Invalid --%s r^2 threshold '%s'.\n",
argptr, argv[cur_arg + param_ct]);
goto main_ret_INVALID_CMDLINE_WWA;
@@ -13546,7 +13574,7 @@ int32_t main(int32_t argc, char** argv) {
} else if (!rel_info.ibc_type) {
rel_info.ibc_type = 1;
}
- retval = plink(outname, outname_end, pedname, mapname, famname,
cm_map_fname, cm_map_chrname, phenoname, extractname, excludename, keepname,
removename, keepfamname, removefamname, filtername, freqname,
distance_wts_fname, read_dists_fname, read_dists_id_fname, evecname,
mergename1, mergename2, mergename3, missing_mid_template,
missing_marker_id_match, makepheno_str, phenoname_str, a1alleles, a2alleles,
recode_allele_name, covar_fname, update_alleles_fname, read_genome_fname,
qual_fi [...]
+ retval = plink(outname, outname_end, pedname, mapname, famname,
cm_map_fname, cm_map_chrname, phenoname, extractname, excludename, keepname,
removename, keepfamname, removefamname, filtername, freqname,
distance_wts_fname, read_dists_fname, read_dists_id_fname, evecname,
mergename1, mergename2, mergename3, missing_mid_template,
missing_marker_id_match, makepheno_str, phenoname_str, a1alleles, a2alleles,
recode_allele_name, covar_fname, update_alleles_fname, read_genome_fname,
qual_fi [...]
}
while (0) {
main_ret_NOMEM:
@@ -13709,6 +13737,7 @@ int32_t main(int32_t argc, char** argv) {
free_cond(metaanal_pfield_search_order);
free_cond(metaanal_essfield_search_order);
free_cond(rplugin_fname);
+ free_cond(rplugin_host_or_socket);
oblig_missing_cleanup(&oblig_missing_info);
cluster_cleanup(&cluster);
diff --git a/plink_calc.c b/plink_calc.c
index 63f76b5..868617a 100644
--- a/plink_calc.c
+++ b/plink_calc.c
@@ -6861,7 +6861,6 @@ int32_t calc_rel(pthread_t* threads, uint32_t
parallel_idx, uint32_t parallel_to
double* main_weights_ptr = nullptr;
double* dptr2;
double set_allele_freq_buf[MULTIPLEX_DIST];
- char wbuf[96];
uint64_t start_offset;
uint64_t hundredth;
unsigned char* overflow_buf;
@@ -7125,19 +7124,20 @@ int32_t calc_rel(pthread_t* threads, uint32_t
parallel_idx, uint32_t parallel_to
if (fputs_checked("FID\tIID\tNOMISS\tFhat1\tFhat2\tFhat3\n", outfile)) {
goto calc_rel_ret_WRITE_FAIL;
}
+ char* textbuf = g_textbuf;
sample_uidx = 0;
for (sample_idx = 0; sample_idx < sample_ct; sample_uidx++, sample_idx++) {
next_unset_ul_unsafe_ck(sample_exclude, &sample_uidx);
fam_id = &(sample_ids[sample_uidx * max_sample_id_len]);
sample_id = (char*)memchr(fam_id, '\t', max_sample_id_len);
- wptr = memcpyax(wbuf, fam_id, (uintptr_t)(sample_id - fam_id), '\t');
+ wptr = memcpyax(textbuf, fam_id, (uintptr_t)(sample_id - fam_id), '\t');
wptr = strcpyax(wptr, &(sample_id[1]), '\t');
wptr = uint32toa_x(marker_ct - sample_missing_unwt[sample_idx], '\t',
wptr);
wptr = dtoa_gx(*dptr3++ - 1.0, '\t', wptr);
wptr = dtoa_gx(*dptr4++ - 1.0, '\t', wptr);
wptr = dtoa_gx(*dptr2++ - 1.0, '\n', wptr);
- if (fwrite_checked(wbuf, wptr - wbuf, outfile)) {
+ if (fwrite_checked(textbuf, wptr - textbuf, outfile)) {
goto calc_rel_ret_WRITE_FAIL;
}
}
diff --git a/plink_common.c b/plink_common.c
index e6b8021..47fa921 100644
--- a/plink_common.c
+++ b/plink_common.c
@@ -4763,7 +4763,7 @@ void chrom_error(const char* chrom_name, const char*
file_descrip, const Chrom_i
if ((raw_code > ((int32_t)chrom_info_ptr->max_code)) && ((raw_code <=
MAX_CHROM_TEXTNUM + XYMT_OFFSET_CT) || (raw_code >= MAX_POSSIBLE_CHROM))) {
if (chrom_info_ptr->species != SPECIES_UNKNOWN) {
if (chrom_info_ptr->species == SPECIES_HUMAN) {
- logerrprint("(This is disallowed for humans. Check if the problem is
with your data, or if\nyou forgot to define a different chromosome set with
e.g. --chr-set.).\n");
+ logerrprint("(This is disallowed for humans. Check if the problem is
with your data, or if\nyou forgot to define a different chromosome set with
e.g. --chr-set.)\n");
} else {
logerrprint("(This is disallowed by the PLINK 1.07 species flag you
used. You can\ntemporarily work around this restriction with --chr-set;
contact the developers\nif you want the flag to be permanently redefined.)\n");
}
diff --git a/plink_data.c b/plink_data.c
index 972aa21..50baef0 100644
--- a/plink_data.c
+++ b/plink_data.c
@@ -246,10 +246,13 @@ int32_t load_map(FILE** mapfile_ptr, char* mapname,
uint32_t* map_cols_ptr, uint
max_marker_id_blen = ulii;
}
if (!unfiltered_marker_ct) {
- textbuf_iter = next_token_mult(textbuf_iter, 2);
+ // bugfix (24 Jul 2017): this was inappropriately erroring out on
+ // 3-column .map files
+ textbuf_iter = next_token(textbuf_iter);
if (!textbuf_iter) {
goto load_map_ret_MISSING_TOKENS;
}
+ textbuf_iter = skip_initial_spaces(token_endnn(textbuf_iter));
if (*textbuf_iter > ' ') {
*map_cols_ptr = 4;
}
@@ -3636,7 +3639,8 @@ int32_t make_bed(FILE* bedfile, uintptr_t bed_offset,
char* bimname, char* outna
goto make_bed_ret_NOMEM;
}
writebuf = (uintptr_t*)g_bigstack_base;
- pass_ct = 1 + ((sample_ctv2 * marker_ct * sizeof(intptr_t) - 1) /
cur_bigstack_left);
+ // 32-bit bugfix (6 Sep 2017): necessary to cast numerator to 64-bit
+ pass_ct = 1 + ((sample_ctv2 * ((uint64_t)marker_ct) * sizeof(intptr_t) -
1) / cur_bigstack_left);
pass_size = 1 + ((marker_ct - 1) / pass_ct);
*outname_end = '\0';
LOGPRINTFWW5("--make-bed to %s.bed + %s.bim + %s.fam ... ", outname,
outname, outname);
@@ -6623,6 +6627,15 @@ int32_t ped_to_bed(char* pedname, char* mapname, char*
outname, char* outname_en
return retval;
}
+uint32_t realpath_identical(const char* outname, const char* read_realpath,
char* write_realpath_buf) {
+#ifdef _WIN32
+ const uint32_t fname_slen = GetFullPathName(outname, FNAMESIZE,
write_realpath_buf, nullptr);
+ return (fname_slen && (fname_slen <= FNAMESIZE) && (!strcmp(read_realpath,
write_realpath_buf)));
+#else
+ return (realpath(outname, write_realpath_buf) && (!strcmp(read_realpath,
write_realpath_buf)));
+#endif
+}
+
int32_t lgen_to_bed(char* lgenname, char* mapname, char* famname, char*
outname, char* outname_end, int32_t missing_pheno, uint64_t misc_flags,
uint32_t lgen_modifier, char* lgen_reference_fname, Chrom_info* chrom_info_ptr)
{
// This code has not been carefully optimized, and also does not support
// multipass writes.
@@ -7143,14 +7156,8 @@ int32_t lgen_to_bed(char* lgenname, char* mapname, char*
famname, char* outname,
LOGERRPRINTFWW("Error: Failed to open %s.\n", outname);
goto lgen_to_bed_ret_OPEN_FAIL;
}
-#ifdef _WIN32
- uii = GetFullPathName(outname, FNAMESIZE, &(g_textbuf[FNAMESIZE + 64]),
nullptr);
- if (!(uii && (uii <= FNAMESIZE) && (!strcmp(g_textbuf, &(g_textbuf[FNAMESIZE
+ 64])))))
-#else
- cptr = realpath(outname, &(g_textbuf[FNAMESIZE + 64]));
- if (!(cptr && (!strcmp(g_textbuf, &(g_textbuf[FNAMESIZE + 64])))))
-#endif
- {
+ // bugfix (25 Jul 2017): forgot the not
+ if (!realpath_identical(outname, g_textbuf, &(g_textbuf[FNAMESIZE + 64]))) {
if (fopen_checked(famname, "r", &infile)) {
goto lgen_to_bed_ret_OPEN_FAIL;
}
diff --git a/plink_data.h b/plink_data.h
index e18e977..4a76e01 100644
--- a/plink_data.h
+++ b/plink_data.h
@@ -34,6 +34,8 @@ int32_t oxford_to_bed(char* genname, char* samplename, char*
outname, char* outn
int32_t ped_to_bed(char* pedname, char* mapname, char* outname, char*
outname_end, uint32_t fam_cols, uint64_t misc_flags, int32_t missing_pheno,
Chrom_info* chrom_info_ptr);
+uint32_t realpath_identical(const char* outname, const char* read_realpath,
char* write_realpath_buf);
+
int32_t lgen_to_bed(char* lgenname, char* mapname, char* famname, char*
outname, char* outname_end, int32_t missing_pheno, uint64_t misc_flags,
uint32_t lgen_modifier, char* lgen_reference_fname, Chrom_info* chrom_info_ptr);
int32_t transposed_to_bed(char* tpedname, char* tfamname, char* outname, char*
outname_end, uint64_t misc_flags, Chrom_info* chrom_info_ptr);
diff --git a/plink_help.c b/plink_help.c
index 6192882..6fcd894 100644
--- a/plink_help.c
+++ b/plink_help.c
@@ -1294,7 +1294,7 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
" it. Also, note that scores are multiplied by 0..1 dosages, not 0..2\n"
" diploid allele counts, unless the 'double-dosage' modifier is
present.\n\n"
);
-#if defined __cplusplus && !defined _WIN32 && !defined STABLE_BUILD
+#if defined __cplusplus && !defined _WIN32
help_print("R\tR-debug", &help_ctrl, 1,
" --R [R script file] <debug>\n"
" Connect to a Rserve (preferably version 1.7 or later) background
process,\n"
@@ -2141,9 +2141,11 @@ int32_t disp_help(uint32_t param_ct, char** argv) {
" j defaults to i+1. The 'header' modifier causes the first nonempty
line\n"
" of this file to be skipped.\n"
);
-#if defined __cplusplus && !defined _WIN32 && !defined STABLE_BUILD
- help_print("R\tR-port", &help_ctrl, 0,
+#if defined __cplusplus && !defined _WIN32
+ help_print("R\tR-port\tR-host\tR-socket", &help_ctrl, 0,
" --R-port [port #] : Connect to Rserve on a port other than 6311.\n"
+" --R-host [host] : Connect to Rserve host.\n"
+" --R-socket [sock] : Connect to Rserve socket.\n"
);
#endif
help_print("parallel\tgenome-lists", &help_ctrl, 0,
diff --git a/plink_lasso.c b/plink_lasso.c
index ba211d8..8338ca7 100644
--- a/plink_lasso.c
+++ b/plink_lasso.c
@@ -26,37 +26,37 @@
#define NLAMBDA 100
#define DELTA_THRESHOLD 0.0001
-int32_t transpose_covar(uintptr_t sample_valid_ct, uintptr_t covar_ct,
uintptr_t* covar_nm, double* readptr, double* writeptr_start, double
sqrt_n_recip, double sample_valid_ct_recip, double sample_valid_ctm1d) {
- // this may migrate to plink_common.c...
+// covar_nm is already subsetted by sample_include
+int32_t transpose_covar(const uintptr_t* sample_exclude, const uintptr_t*
pheno_nm, const uintptr_t* covar_nm, const double* readptr, uint32_t sample_ct,
uintptr_t sample_valid_ct, uintptr_t covar_ct, double sqrt_n_recip, double
sample_valid_ct_recip, double sample_valid_ctm1d, double* writeptr_start) {
double sum = 0.0;
double ssq = 0.0;
double* writeptr = writeptr_start;
- uintptr_t sample_uidx;
- uintptr_t sample_idx;
- double subtract_by;
- double multiply_by;
- double dxx;
- for (sample_uidx = 0, sample_idx = 0; sample_idx < sample_valid_ct;
sample_uidx++, sample_idx++) {
- next_set_ul_unsafe_ck(covar_nm, &sample_uidx);
- dxx = readptr[sample_uidx * covar_ct];
- sum += dxx;
- ssq += dxx * dxx;
- *writeptr++ = dxx;
+ uint32_t sample_uidx = 0;
+ uint32_t uii = 0;
+ for (uint32_t sample_idx = 0; sample_idx < sample_ct; ++sample_uidx,
++sample_idx) {
+ next_unset_unsafe_ck(sample_exclude, &sample_uidx);
+ if (IS_SET(pheno_nm, sample_uidx)) {
+ const double dxx = readptr[sample_idx * covar_ct];
+ sum += dxx;
+ ssq += dxx * dxx;
+ *writeptr++ = dxx;
+ ++uii;
+ }
}
if (ssq * ((double)sample_valid_ct) == sum * sum) {
return -1;
}
- subtract_by = sum * sample_valid_ct_recip;
- multiply_by = sqrt_n_recip * sqrt(sample_valid_ctm1d / (ssq - sum *
subtract_by));
+ const double subtract_by = sum * sample_valid_ct_recip;
+ const double multiply_by = sqrt_n_recip * sqrt(sample_valid_ctm1d / (ssq -
sum * subtract_by));
writeptr = writeptr_start;
- for (sample_idx = 0; sample_idx < sample_valid_ct; sample_idx++) {
+ for (uint32_t sample_idx = 0; sample_idx < sample_valid_ct; ++sample_idx) {
*writeptr = ((*writeptr) - subtract_by) * multiply_by;
writeptr++;
}
return 0;
}
-int32_t lasso_bigmem(FILE* bedfile, uintptr_t bed_offset, uintptr_t*
marker_exclude, uintptr_t marker_ct, uintptr_t* marker_reverse, Chrom_info*
chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm2, double
lasso_h2, double lasso_minlambda, uint32_t select_covars, uintptr_t*
select_covars_bitfield, double* pheno_d_collapsed, uintptr_t covar_ct, char*
covar_names, uintptr_t max_covar_name_len, uintptr_t* covar_nm, double*
covar_d, uint32_t hh_or_mt_exists, uintptr_t sample_ [...]
+int32_t lasso_bigmem(FILE* bedfile, uintptr_t bed_offset, uintptr_t*
marker_exclude, uintptr_t marker_ct, uintptr_t* marker_reverse, Chrom_info*
chrom_info_ptr, uintptr_t unfiltered_sample_ct, const uintptr_t*
sample_exclude, uintptr_t* pheno_nm2, double lasso_h2, double lasso_minlambda,
uint32_t select_covars, uintptr_t* select_covars_bitfield, double*
pheno_d_collapsed, uintptr_t covar_ct, char* covar_names, uintptr_t
max_covar_name_len, uintptr_t* covar_nm, double* covar_d, uint32_t h [...]
uintptr_t unfiltered_sample_ct4 = (unfiltered_sample_ct + 3) / 4;
double* data_arr = (double*)g_bigstack_base; // marker-major
double sqrt_n_recip = sqrt(1.0 / ((double)((intptr_t)sample_valid_ct)));
@@ -127,7 +127,7 @@ int32_t lasso_bigmem(FILE* bedfile, uintptr_t bed_offset,
uintptr_t* marker_excl
dyy = (double)((intptr_t)(sample_valid_ct - 1));
if (!select_covars_bitfield) {
for (covar_idx = 0; covar_idx < covar_ct; covar_idx++) {
- if (transpose_covar(sample_valid_ct, covar_ct, covar_nm,
&(covar_d[covar_idx]), &(data_arr[covar_idx * sample_valid_ct]), sqrt_n_recip,
dxx, dyy)) {
+ if (transpose_covar(sample_exclude, pheno_nm2, covar_nm,
&(covar_d[covar_idx]), sample_ct, sample_valid_ct, covar_ct, sqrt_n_recip, dxx,
dyy, &(data_arr[covar_idx * sample_valid_ct]))) {
goto lasso_bigmem_ret_CONST_COVAR;
}
}
@@ -140,7 +140,7 @@ int32_t lasso_bigmem(FILE* bedfile, uintptr_t bed_offset,
uintptr_t* marker_excl
if (IS_SET(select_covars_bitfield, covar_idx)) {
continue;
}
- if (transpose_covar(sample_valid_ct, covar_ct, covar_nm,
&(covar_d[covar_idx]), &(data_arr[ulii * sample_valid_ct]), sqrt_n_recip, dxx,
dyy)) {
+ if (transpose_covar(sample_exclude, pheno_nm2, covar_nm,
&(covar_d[covar_idx]), sample_ct, sample_valid_ct, covar_ct, sqrt_n_recip, dxx,
dyy, &(data_arr[ulii * sample_valid_ct]))) {
goto lasso_bigmem_ret_CONST_COVAR;
}
ulii++;
@@ -150,7 +150,7 @@ int32_t lasso_bigmem(FILE* bedfile, uintptr_t bed_offset,
uintptr_t* marker_excl
if (!IS_SET(select_covars_bitfield, covar_idx)) {
continue;
}
- if (transpose_covar(sample_valid_ct, covar_ct, covar_nm,
&(covar_d[covar_idx]), &(data_arr[ulii * sample_valid_ct]), sqrt_n_recip, dxx,
dyy)) {
+ if (transpose_covar(sample_exclude, pheno_nm2, covar_nm,
&(covar_d[covar_idx]), sample_ct, sample_valid_ct, covar_ct, sqrt_n_recip, dxx,
dyy, &(data_arr[ulii * sample_valid_ct]))) {
goto lasso_bigmem_ret_CONST_COVAR;
}
ulii++;
@@ -429,37 +429,33 @@ uint32_t load_and_normalize(FILE* bedfile, uintptr_t*
loadbuf_raw, uintptr_t unf
// this needs to work in very-low-memory contexts
#define LASSO_LAMBDA_BLOCK_SIZE 64
-int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t*
marker_reverse, Chrom_info* chrom_info_ptr, uintptr_t* sex_male, uintptr_t*
pheno_nm, const uintptr_t* covar_nm, uintptr_t bed_offset, uintptr_t
unfiltered_marker_ct, uintptr_t marker_ct, uintptr_t unfiltered_sample_ct,
uintptr_t pheno_nm_ct, uint32_t hh_or_mt_exists, uint32_t lasso_lambda_iters,
double lasso_h2, FILE* bedfile, char* outname, char* outname_end, double*
lasso_minlambda_ptr) {
+int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t*
marker_reverse, Chrom_info* chrom_info_ptr, const uintptr_t* sample_exclude,
uintptr_t* sex_male, uintptr_t* pheno_nm, const uintptr_t* covar_nm, uintptr_t
bed_offset, uintptr_t unfiltered_marker_ct, uintptr_t marker_ct, uintptr_t
unfiltered_sample_ct, uint32_t sample_ct, uintptr_t pheno_nm_ct, uint32_t
hh_or_mt_exists, uint32_t lasso_lambda_iters, double lasso_h2, FILE* bedfile,
char* outname, char* outname_end, doub [...]
// standalone memory-efficient lambda calculation, since even 1000 x
// sample_ct matrices may be too large.
unsigned char* bigstack_mark = g_bigstack_base;
FILE* outfile = nullptr;
int32_t retval = 0;
{
+ const uintptr_t unfiltered_sample_ctl =
BITCT_TO_WORDCT(unfiltered_sample_ct);
+ uintptr_t* pheno_nm2;
uintptr_t sample_valid_ct;
if (!covar_nm) {
sample_valid_ct = pheno_nm_ct;
- } else {
- sample_valid_ct = popcount_longs(covar_nm, BITCT_TO_WORDCT(pheno_nm_ct));
- }
- const uintptr_t final_mask = get_final_mask(sample_valid_ct);
- uintptr_t* pheno_nm2;
- if (sample_valid_ct == pheno_nm_ct) {
pheno_nm2 = pheno_nm;
} else {
- const uintptr_t unfiltered_sample_ctl =
BITCT_TO_WORDCT(unfiltered_sample_ct);
if (bigstack_calloc_ul(unfiltered_sample_ctl, &pheno_nm2)) {
goto lasso_lambda_ret_NOMEM;
}
- uintptr_t sample_uidx;
- uintptr_t sample_idx;
- for (sample_uidx = 0, sample_idx = 0; sample_idx < pheno_nm_ct;
sample_uidx++, sample_idx++) {
- next_set_ul_unsafe_ck(pheno_nm, &sample_uidx);
- if (IS_SET(covar_nm, sample_idx)) {
+ uintptr_t sample_uidx = 0;
+ for (uintptr_t sample_idx = 0; sample_idx < sample_ct; ++sample_uidx,
++sample_idx) {
+ next_unset_ul_unsafe_ck(sample_exclude, &sample_uidx);
+ if (IS_SET(pheno_nm, sample_uidx) && IS_SET(covar_nm, sample_idx)) {
SET_BIT(sample_uidx, pheno_nm2);
}
}
+ sample_valid_ct = popcount_longs(pheno_nm2, unfiltered_sample_ctl);
}
+ const uintptr_t final_mask = get_final_mask(sample_valid_ct);
double* rand_matrix;
double* max_empirical_lambdas;
double* data_window;
@@ -636,7 +632,7 @@ int32_t lasso_lambda(const uintptr_t* marker_exclude, const
uintptr_t* marker_re
}
-int32_t lasso_smallmem(pthread_t* threads, FILE* bedfile, uintptr_t
bed_offset, uintptr_t* marker_exclude, uintptr_t marker_ct, uintptr_t*
marker_reverse, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct,
uintptr_t* pheno_nm2, double lasso_h2, double lasso_minlambda, uint32_t
select_covars, uintptr_t* select_covars_bitfield, double* pheno_d_collapsed,
uintptr_t covar_ct, char* covar_names, uintptr_t max_covar_name_len, uintptr_t*
covar_nm, double* covar_d, uint32_t hh_or_mt_exi [...]
+int32_t lasso_smallmem(pthread_t* threads, FILE* bedfile, uintptr_t
bed_offset, uintptr_t* marker_exclude, uintptr_t marker_ct, uintptr_t*
marker_reverse, Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct,
const uintptr_t* sample_exclude, uintptr_t* pheno_nm2, double lasso_h2, double
lasso_minlambda, uint32_t select_covars, uintptr_t* select_covars_bitfield,
double* pheno_d_collapsed, uintptr_t covar_ct, char* covar_names, uintptr_t
max_covar_name_len, uintptr_t* covar_nm, doubl [...]
// Instead of populating and normalizing data_arr before the coordinate
// descent, we reload and renormalize the data every iteration.
// Since (i) there's probably a larger number of samples involved, and (ii)
@@ -703,7 +699,7 @@ int32_t lasso_smallmem(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset,
dyy = (double)((intptr_t)(sample_valid_ct - 1));
if (!select_covars_bitfield) {
for (covar_idx = 0; covar_idx < covar_ct; covar_idx++) {
- if (transpose_covar(sample_valid_ct, covar_ct, covar_nm,
&(covar_d[covar_idx]), &(covar_data_arr[covar_idx * sample_valid_ct]),
sqrt_n_recip, dxx, dyy)) {
+ if (transpose_covar(sample_exclude, pheno_nm2, covar_nm,
&(covar_d[covar_idx]), sample_ct, sample_valid_ct, covar_ct, sqrt_n_recip, dxx,
dyy, &(covar_data_arr[covar_idx * sample_valid_ct]))) {
goto lasso_smallmem_ret_CONST_COVAR;
}
}
@@ -716,7 +712,7 @@ int32_t lasso_smallmem(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset,
if (IS_SET(select_covars_bitfield, covar_idx)) {
continue;
}
- if (transpose_covar(sample_valid_ct, covar_ct, covar_nm,
&(covar_d[covar_idx]), &(covar_data_arr[ulii * sample_valid_ct]), sqrt_n_recip,
dxx, dyy)) {
+ if (transpose_covar(sample_exclude, pheno_nm2, covar_nm,
&(covar_d[covar_idx]), sample_ct, sample_valid_ct, covar_ct, sqrt_n_recip, dxx,
dyy, &(covar_data_arr[ulii * sample_valid_ct]))) {
goto lasso_smallmem_ret_CONST_COVAR;
}
ulii++;
@@ -726,7 +722,7 @@ int32_t lasso_smallmem(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset,
if (!IS_SET(select_covars_bitfield, covar_idx)) {
continue;
}
- if (transpose_covar(sample_valid_ct, covar_ct, covar_nm,
&(covar_d[covar_idx]), &(covar_data_arr[ulii * sample_valid_ct]), sqrt_n_recip,
dxx, dyy)) {
+ if (transpose_covar(sample_exclude, pheno_nm2, covar_nm,
&(covar_d[covar_idx]), sample_ct, sample_valid_ct, covar_ct, sqrt_n_recip, dxx,
dyy, &(covar_data_arr[ulii * sample_valid_ct]))) {
goto lasso_smallmem_ret_CONST_COVAR;
}
ulii++;
@@ -995,16 +991,16 @@ int32_t lasso_smallmem(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset,
return retval;
}
-int32_t lasso(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*
outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t*
marker_exclude, uintptr_t marker_ct, char* marker_ids, uintptr_t
max_marker_id_len, char** marker_allele_ptrs, uintptr_t* marker_reverse,
Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t
pheno_nm_ct, double lasso_h2, double lasso_minlambda, Range_list*
select_covars_range_list_ptr, uint64_t misc_flags, uintptr_t* pheno_nm [...]
+int32_t lasso(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*
outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t*
marker_exclude, uintptr_t marker_ct, char* marker_ids, uintptr_t
max_marker_id_len, char** marker_allele_ptrs, uintptr_t* marker_reverse,
Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uint32_t sample_ct,
uintptr_t pheno_nm_ct, double lasso_h2, double lasso_minlambda, Range_list*
select_covars_range_list_ptr, uint64_t misc_flags, [...]
// Coordinate descent LASSO. Based on a MATLAB script by Shashaank
// Vattikuti.
// Not yet multithreaded. (Main loop is fairly tightly coupled, so getting
// a performance benefit will be a bit tricky.)
unsigned char* bigstack_mark = g_bigstack_base;
FILE* outfile = nullptr;
- uintptr_t unfiltered_sample_ctl = BITCT_TO_WORDCT(unfiltered_sample_ct);
- uintptr_t unfiltered_sample_ctv2 =
QUATERCT_TO_ALIGNED_WORDCT(unfiltered_sample_ct);
- uintptr_t unfiltered_marker_ctl = BITCT_TO_WORDCT(unfiltered_marker_ct);
+ const uintptr_t unfiltered_sample_ctl =
BITCT_TO_WORDCT(unfiltered_sample_ct);
+ const uintptr_t unfiltered_sample_ctv2 =
QUATERCT_TO_ALIGNED_WORDCT(unfiltered_sample_ct);
+ const uintptr_t unfiltered_marker_ctl =
BITCT_TO_WORDCT(unfiltered_marker_ct);
uintptr_t polymorphic_marker_ct = 0;
uint64_t iter_tot = 0;
double* xhat = nullptr;
@@ -1013,8 +1009,8 @@ int32_t lasso(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset, char* out
uintptr_t* sample_male_include2 = nullptr;
uintptr_t* select_covars_bitfield = nullptr;
char* wptr_start = nullptr;
- uint32_t report_zeroes = (misc_flags / MISC_LASSO_REPORT_ZEROES) & 1;
- uint32_t select_covars = (misc_flags / MISC_LASSO_SELECT_COVARS) & 1;
+ const uint32_t report_zeroes = (misc_flags / MISC_LASSO_REPORT_ZEROES) & 1;
+ const uint32_t select_covars = (misc_flags / MISC_LASSO_SELECT_COVARS) & 1;
uint32_t chrom_fo_idx = 0xffffffffU; // exploit overflow
uint32_t chrom_end = 0;
uint32_t is_x = 0;
@@ -1052,8 +1048,22 @@ int32_t lasso(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset, char* out
uint32_t uii;
if (!covar_ct) {
sample_valid_ct = pheno_nm_ct;
+ pheno_nm2 = pheno_nm;
} else {
- sample_valid_ct = popcount_longs(covar_nm, BITCT_TO_WORDCT(pheno_nm_ct));
+ // bugfix (14 Aug 2017): need to look at intersection of pheno_nm and
+ // covar_nm, rather than just covar_nm
+ // also, can't simply use popcount_longs_intersect() and bitvec_and(),
+ // since covar_nm is already subsetted on sample_include
+ if (bigstack_calloc_ul(unfiltered_sample_ctl, &pheno_nm2)) {
+ goto lasso_ret_NOMEM;
+ }
+ for (sample_uidx = 0, sample_idx = 0; sample_idx < sample_ct;
sample_uidx++, sample_idx++) {
+ next_unset_ul_unsafe_ck(sample_exclude, &sample_uidx);
+ if (IS_SET(pheno_nm, sample_uidx) && IS_SET(covar_nm, sample_idx)) {
+ SET_BIT(sample_uidx, pheno_nm2);
+ }
+ }
+ sample_valid_ct = popcount_longs(pheno_nm2, unfiltered_sample_ctl);
}
if (sample_valid_ct < 2) {
if (pheno_nm_ct < 2) {
@@ -1063,19 +1073,6 @@ int32_t lasso(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset, char* out
}
goto lasso_ret_1;
}
- if (sample_valid_ct == pheno_nm_ct) {
- pheno_nm2 = pheno_nm;
- } else {
- if (bigstack_calloc_ul(unfiltered_sample_ctl, &pheno_nm2)) {
- goto lasso_ret_NOMEM;
- }
- for (sample_uidx = 0, sample_idx = 0; sample_idx < pheno_nm_ct;
sample_uidx++, sample_idx++) {
- next_set_ul_unsafe_ck(pheno_nm, &sample_uidx);
- if (IS_SET(covar_nm, sample_idx)) {
- SET_BIT(sample_uidx, pheno_nm2);
- }
- }
- }
sample_valid_ctv2 = QUATERCT_TO_ALIGNED_WORDCT(sample_valid_ct);
sqrt_n_recip = sqrt(1.0 / ((double)((intptr_t)sample_valid_ct)));
if (bigstack_alloc_ul(sample_valid_ctv2, &sample_include2) ||
@@ -1179,9 +1176,9 @@ int32_t lasso(pthread_t* threads, FILE* bedfile,
uintptr_t bed_offset, char* out
}
ullii += round_up_pow2(((uint64_t)uii) * sample_valid_ct * sizeof(double),
CACHELINE);
if (ullii <= bigstack_left()) {
- retval = lasso_bigmem(bedfile, bed_offset, marker_exclude, marker_ct,
marker_reverse, chrom_info_ptr, unfiltered_sample_ct, pheno_nm2, lasso_h2,
lasso_minlambda, select_covars, select_covars_bitfield, pheno_d_collapsed,
covar_ct, covar_names, max_covar_name_len, covar_nm, covar_d, hh_or_mt_exists,
sample_valid_ct, sample_include2, sample_male_include2, loadbuf_raw,
loadbuf_collapsed, rand_matrix, misc_arr, residuals, polymorphic_markers,
&polymorphic_marker_ct, &iter_tot, &xhat);
+ retval = lasso_bigmem(bedfile, bed_offset, marker_exclude, marker_ct,
marker_reverse, chrom_info_ptr, unfiltered_sample_ct, sample_exclude,
pheno_nm2, lasso_h2, lasso_minlambda, select_covars, select_covars_bitfield,
pheno_d_collapsed, covar_ct, covar_names, max_covar_name_len, covar_nm,
covar_d, hh_or_mt_exists, sample_ct, sample_valid_ct, sample_include2,
sample_male_include2, loadbuf_raw, loadbuf_collapsed, rand_matrix, misc_arr,
residuals, polymorphic_markers, &polymorphic_marker [...]
} else {
- retval = lasso_smallmem(threads, bedfile, bed_offset, marker_exclude,
marker_ct, marker_reverse, chrom_info_ptr, unfiltered_sample_ct, pheno_nm2,
lasso_h2, lasso_minlambda, select_covars, select_covars_bitfield,
pheno_d_collapsed, covar_ct, covar_names, max_covar_name_len, covar_nm,
covar_d, hh_or_mt_exists, sample_valid_ct, sample_include2,
sample_male_include2, loadbuf_raw, loadbuf_collapsed, rand_matrix, misc_arr,
residuals, polymorphic_markers, &polymorphic_marker_ct, &iter_tot, &xhat);
+ retval = lasso_smallmem(threads, bedfile, bed_offset, marker_exclude,
marker_ct, marker_reverse, chrom_info_ptr, unfiltered_sample_ct,
sample_exclude, pheno_nm2, lasso_h2, lasso_minlambda, select_covars,
select_covars_bitfield, pheno_d_collapsed, covar_ct, covar_names,
max_covar_name_len, covar_nm, covar_d, hh_or_mt_exists, sample_ct,
sample_valid_ct, sample_include2, sample_male_include2, loadbuf_raw,
loadbuf_collapsed, rand_matrix, misc_arr, residuals, polymorphic_markers,
&polymor [...]
}
if (retval || (!polymorphic_marker_ct)) {
goto lasso_ret_1;
diff --git a/plink_lasso.h b/plink_lasso.h
index 3227f03..7c39e9a 100644
--- a/plink_lasso.h
+++ b/plink_lasso.h
@@ -18,8 +18,8 @@
// along with this program. If not, see <http://www.gnu.org/licenses/>.
-int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t*
marker_reverse, Chrom_info* chrom_info_ptr, uintptr_t* sex_male, uintptr_t*
pheno_nm, const uintptr_t* covar_nm, uintptr_t bed_offset, uintptr_t
unfiltered_marker_ct, uintptr_t marker_ct, uintptr_t unfiltered_sample_ct,
uintptr_t pheno_nm_ct, uint32_t hh_or_mt_exists, uint32_t lasso_lambda_iters,
double lasso_h2, FILE* bedfile, char* outname, char* outname_end, double*
lasso_minlambda_ptr);
+int32_t lasso_lambda(const uintptr_t* marker_exclude, const uintptr_t*
marker_reverse, Chrom_info* chrom_info_ptr, const uintptr_t* sample_exclude,
uintptr_t* sex_male, uintptr_t* pheno_nm, const uintptr_t* covar_nm, uintptr_t
bed_offset, uintptr_t unfiltered_marker_ct, uintptr_t marker_ct, uintptr_t
unfiltered_sample_ct, uint32_t sample_ct, uintptr_t pheno_nm_ct, uint32_t
hh_or_mt_exists, uint32_t lasso_lambda_iters, double lasso_h2, FILE* bedfile,
char* outname, char* outname_end, doub [...]
-int32_t lasso(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*
outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t*
marker_exclude, uintptr_t marker_ct, char* marker_ids, uintptr_t
max_marker_id_len, char** marker_allele_ptrs, uintptr_t* marker_reverse,
Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t
pheno_nm_ct, double lasso_h2, double lasso_minlambda, Range_list*
select_covars_range_list_ptr, uint64_t misc_flags, uintptr_t* pheno_nm [...]
+int32_t lasso(pthread_t* threads, FILE* bedfile, uintptr_t bed_offset, char*
outname, char* outname_end, uintptr_t unfiltered_marker_ct, uintptr_t*
marker_exclude, uintptr_t marker_ct, char* marker_ids, uintptr_t
max_marker_id_len, char** marker_allele_ptrs, uintptr_t* marker_reverse,
Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uint32_t sample_ct,
uintptr_t pheno_nm_ct, double lasso_h2, double lasso_minlambda, Range_list*
select_covars_range_list_ptr, uint64_t misc_flags, [...]
#endif // __PLINK_LASSO_H__
diff --git a/plink_rserve.c b/plink_rserve.c
index 5d1aa6c..7658a50 100644
--- a/plink_rserve.c
+++ b/plink_rserve.c
@@ -30,7 +30,7 @@
#define RPLUGIN_BLOCK_SIZE 100
-int32_t rserve_call(char* rplugin_fname, uint32_t rplugin_port, uint32_t
rplugin_debug, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct,
uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t*
marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, char**
marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info*
chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm, uint32_t
pheno_nm_ct, uintptr_t* pheno_c, double* pheno_d, u [...]
+int32_t rserve_call(char* rplugin_fname, char* rplugin_host_or_socket, int32_t
rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_offset,
uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude,
uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len,
char** marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp,
Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t*
pheno_nm, uint32_t pheno_nm_ct, uintptr_t [...]
// See PLINK 1.07 r.cpp.
unsigned char* bigstack_mark = g_bigstack_base;
FILE* infile = nullptr;
@@ -180,7 +180,10 @@ int32_t rserve_call(char* rplugin_fname, uint32_t
rplugin_port, uint32_t rplugin
if (bigstack_alloc_i(RPLUGIN_BLOCK_SIZE * ((uintptr_t)pheno_nm_ct),
&geno_int_buf)) {
goto rserve_call_ret_NOMEM;
}
- rc = new Rconnection("127.0.0.1", rplugin_port);
+ if (rplugin_port == -2) {
+ rplugin_port = 6311;
+ }
+ rc = new Rconnection(rplugin_host_or_socket, rplugin_port);
ii = rc->connect();
if (ii) {
sockerrorchecks(g_textbuf, 128, -1);
diff --git a/plink_rserve.h b/plink_rserve.h
index 7895873..de9bdcc 100644
--- a/plink_rserve.h
+++ b/plink_rserve.h
@@ -18,6 +18,6 @@
// along with this program. If not, see <http://www.gnu.org/licenses/>.
-int32_t rserve_call(char* rplugin_fname, uint32_t rplugin_port, uint32_t
rplugin_debug, FILE* bedfile, uintptr_t bed_offset, uintptr_t marker_ct,
uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude, uintptr_t*
marker_reverse, char* marker_ids, uintptr_t max_marker_id_len, char**
marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp, Chrom_info*
chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t* pheno_nm, uint32_t
pheno_nm_ct, uintptr_t* pheno_c, double* pheno_d, u [...]
+int32_t rserve_call(char* rplugin_fname, char* rplugin_host_or_socket, int32_t
rplugin_port, uint32_t rplugin_debug, FILE* bedfile, uintptr_t bed_offset,
uintptr_t marker_ct, uintptr_t unfiltered_marker_ct, uintptr_t* marker_exclude,
uintptr_t* marker_reverse, char* marker_ids, uintptr_t max_marker_id_len,
char** marker_allele_ptrs, uint32_t* marker_pos, uint32_t plink_maxsnp,
Chrom_info* chrom_info_ptr, uintptr_t unfiltered_sample_ct, uintptr_t*
pheno_nm, uint32_t pheno_nm_ct, uintptr_t [...]
#endif // __PLINK_RSERVE_H__
--
Alioth's /usr/local/bin/git-commit-notice on
/srv/git.debian.org/git/debian-med/plink1.9.git
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