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From: Robert May <tpibob@gmail.com>
To: "cygwin@cygwin.com" <cygwin@cygwin.com>
Subject: bcftools error running Make after installing update 2.4.1.1 to Cygwin64
Date: Mon, 25 Jan 2016 21:11:00 -0000
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error running Make after installing update 2.4.1.1 to Cygwin64

Robert@DESKTOP-14EL82S /usr/local/bin/bcftools-1.3

$ make
=A0
many warnings are given in the following text - see end for error message

echo '#define BCFTOOLS_VERSION "1.3"'> version.h
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o main.o main.c
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfindex.o vcfindex.c
vcfindex.c: In function =91main_vcfindex=92:
vcfindex.c:209:9: warning: implicit declaration of function =91alloca=92 [-=
Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 char *idx_fname =3D (char*)alloca(strlen(fname) + =
5);
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfindex.c:209:27: warning: cast to pointer from integer of different size =
[-Wint-to-pointer-cast]
=A0=A0=A0=A0=A0=A0=A0=A0 char *idx_fname =3D (char*)alloca(strlen(fname) + =
5);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o tabix.o tabix.c
tabix.c: In function =91main_tabix=92:
tabix.c:97:13: warning: implicit declaration of function =91alloca=92 [-Wim=
plicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 fn =3D (char*)alloca(strlen(argv[optin=
d]) + 5);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
tabix.c:97:18: warning: cast to pointer from integer of different size [-Wi=
nt-to-pointer-cast]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 fn =3D (char*)alloca(strlen(argv[optin=
d]) + 5);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfstats.o vcfstats.c
vcfstats.c: In function =91main_vcfstats=92:
vcfstats.c:1558:9: warning: implicit declaration of function =91fileno=92 [=
-Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfisec.o vcfisec.c
vcfisec.c: In function =91main_vcfisec=92:
vcfisec.c:556:21: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 else if ( isdi=
git(*p) ) args->isec_op =3D OP_EQUAL;
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfmerge.o vcfmerge.c
vcfmerge.c: In function =91merge_alleles=92:
vcfmerge.c:542:13: warning: array subscript has type =91char=92 [-Wchar-sub=
scripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 for (j=3D0; j<len; j++) a[i][j] =3D to=
upper(a[i][j]);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfmerge.c:547:13: warning: array subscript has type =91char=92 [-Wchar-sub=
scripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 for (j=3D0; j<len; j++) b[i][j] =3D to=
upper(b[i][j]);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfquery.o vcfquery.c
vcfquery.c: In function =91main_vcfquery=92:
vcfquery.c:285:9: warning: implicit declaration of function =91fileno=92 [-=
Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcffilter.o vcffilter.c
vcffilter.c: In function =91main_vcffilter=92:
vcffilter.c:501:9: warning: implicit declaration of function =91fileno=92 [=
-Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o filter.o filter.c
filter.c: In function =91filters_next_token=92:
filter.c:109:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 while ( *tmp && isspace(*tmp) ) tmp++;
=A0=A0=A0=A0 ^
filter.c:114:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 if ( isdigit(*str[0]) || *str[0]=3D=3D'.' )=A0=A0 // strtod wo=
uld eat +/-
=A0=A0=A0=A0 ^
filter.c:117:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( *str!=3Dtmp && (!tmp[0] || !isalnum(tmp[0])) )
=A0=A0=A0=A0=A0=A0=A0=A0 ^
filter.c:141:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *tmp && !isspace(*tmp) && *tmp!=3D'=3D' &&=
 *tmp!=3D'!' ) tmp++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
filter.c:150:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( isspace(tmp[0]) ) break;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
filter.c: In function =91filters_init1=92:
filter.c:1173:13: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
filter.c: In function =91filter_init=92:
filter.c:1479:13: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( *tmp && !isspace(*tmp) ) error("C=
ould not parse the expression: [%s]\n", str);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfsom.o vcfsom.c
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfnorm.o vcfnorm.c
vcfnorm.c: In function =91replace_iupac_codes=92:
vcfnorm.c:88:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 char c =3D toupper(seq[i]);
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfnorm.c: In function =91main_vcfnorm=92:
vcfnorm.c:1785:9: warning: implicit declaration of function =91fileno=92 [-=
Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfgtcheck.o vcfgtcheck.c
vcfgtcheck.c: In function =91main_vcfgtcheck=92:
vcfgtcheck.c:780:9: warning: implicit declaration of function =91fileno=92 =
[-Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfview.o vcfview.c
vcfview.c: In function =91main_vcfview=92:
vcfview.c:696:9: warning: implicit declaration of function =91fileno=92 [-W=
implicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfannotate.o vcfannotate.c
vcfannotate.c: In function =91set_samples=92:
vcfannotate.c:1033:9: warning: array subscript has type =91char=92 [-Wchar-=
subscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfannotate.c:1049:9: warning: array subscript has type =91char=92 [-Wchar-=
subscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( isspace(*ss) ) ss++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfannotate.c:1051:9: warning: array subscript has type =91char=92 [-Wchar-=
subscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfannotate.c: In function =91rename_chrs=92:
vcfannotate.c:1357:9: warning: array subscript has type =91char=92 [-Wchar-=
subscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *ss && !isspace(*ss) ) ss++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfannotate.c:1367:9: warning: array subscript has type =91char=92 [-Wchar-=
subscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *ss && isspace(*ss) ) ss++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfannotate.c:1369:9: warning: array subscript has type =91char=92 [-Wchar-=
subscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfannotate.c: In function =91main_vcfannotate=92:
vcfannotate.c:1716:9: warning: implicit declaration of function =91fileno=
=92 [-Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfroh.o vcfroh.c
vcfroh.c: In function =91load_genmap=92:
vcfroh.c:229:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *tmp && !isspace(*tmp) ) tmp++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfroh.c: In function =91read_AF=92:
vcfroh.c:439:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 if ( *tmp && !isspace(*tmp) )
=A0=A0=A0=A0 ^
vcfroh.c:441:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( str[0]=3D=3D'.' && (!str[1] || isspace(str[1]=
)) ) return -1; // missing value
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfconcat.o vcfconcat.c
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfcall.o vcfcall.c
vcfcall.c: In function =91parse_ped_samples=92:
vcfcall.c:201:13: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( isspace(*tmp) )
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcall.c:205:17: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 while ( isspace(*tmp) ) tm=
p++;=A0 // allow multiple spaces
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcall.c: In function =91set_samples=92:
vcfcall.c:283:9: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *ss && isspace(*ss) ) ss++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcall.c:287:9: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcall.c:294:9: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *ss && isspace(*ss) ) ss++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcall.c:297:9: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcall.c: In function =91main_vcfcall=92:
vcfcall.c:739:9: warning: implicit declaration of function =91fileno=92 [-W=
implicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fna=
me =3D "-";=A0 // reading from stdin
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o mcall.o mcall.c
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcmp.o vcmp.c
vcmp.c: In function =91vcmp_set_ref=92:
vcmp.c:57:5: warning: array subscript has type =91char=92 [-Wchar-subscript=
s]
=A0=A0=A0=A0 while ( *a && *b && toupper(*a)=3D=3Dtoupper(*b) ) { a++; b++;=
 }
=A0=A0=A0=A0 ^
vcmp.c:57:5: warning: array subscript has type =91char=92 [-Wchar-subscript=
s]
vcmp.c:68:9: warning: array subscript has type =91char=92 [-Wchar-subscript=
s]
=A0=A0=A0=A0=A0=A0=A0=A0 for (i=3D0; i<vcmp->ndref; i++) vcmp->dref[i] =3D =
toupper(ref1[vcmp->nmatch+i]);
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcmp.c:78:5: warning: array subscript has type =91char=92 [-Wchar-subscript=
s]
=A0=A0=A0=A0 for (i=3D0; i<vcmp->ndref; i++) vcmp->dref[i] =3D toupper(ref2=
[vcmp->nmatch+i]);
=A0=A0=A0=A0 ^
vcmp.c: In function =91vcmp_find_allele=92:
vcmp.c:90:9: warning: array subscript has type =91char=92 [-Wchar-subscript=
s]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *a && *b && toupper(*a)=3D=3Dtoupper(*b) )=
 { a++; b++; }
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcmp.c:90:9: warning: array subscript has type =91char=92 [-Wchar-subscript=
s]
vcmp.c:103:17: warning: array subscript has type =91char=92 [-Wchar-subscri=
pts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( !a[j] || toupper(a[j]=
)!=3Dvcmp->dref[j] ) break;
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcmp.c:110:13: warning: array subscript has type =91char=92 [-Wchar-subscri=
pts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( !b[j] || toupper(b[j])!=3Dvcmp->d=
ref[j] ) break;
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o gvcf.o gvcf.c
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o reheader.o reheader.c
reheader.c: In function =91read_header_file=92:
reheader.c:65:5: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0 while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;=A0 /=
/ remove trailing newlines
=A0=A0=A0=A0 ^
reheader.c: In function =91set_sample_pairs=92:
reheader.c:79:9: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *value && !isspace(*value) ) value++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
reheader.c:82:9: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( isspace(*value) ) value++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
reheader.c:91:5: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0 while ( hdr->l>0 && isspace(hdr->s[hdr->l-1]) ) hdr->l--;=A0 /=
/ remove trailing newlines
=A0=A0=A0=A0 ^
reheader.c: In function =91reheader_vcf_gz=92:
reheader.c:227:9: warning: implicit declaration of function =91fileno=92 [-=
Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 bgzf_out =3D bgzf_dopen(fileno(stdout), "w");
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o convert.o convert.c
convert.c: In function =91parse_subscript=92:
convert.c:781:5: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0 while ( *q && *q!=3D'}' && isdigit(*q) ) q++;
=A0=A0=A0=A0 ^
convert.c: In function =91parse_tag=92:
convert.c:791:5: warning: array subscript has type =91char=92 [-Wchar-subsc=
ripts]
=A0=A0=A0=A0 while ( *q && (isalnum(*q) || *q=3D=3D'_' || *q=3D=3D'.') ) q+=
+;
=A0=A0=A0=A0 ^
convert.c:806:13: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 while ( *q && (isalnum(*q) || *q=3D=3D=
'_' || *q=3D=3D'.') ) q++;
=A0^
convert.c:848:13: warning: array subscript has type =91char=92 [-Wchar-subs=
cripts]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 while ( *q && (isalnum(*q) || *q=3D=3D=
'_' || *q=3D=3D'.') ) q++;
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfconvert.o vcfconvert.c
In file included from vcfconvert.c:42:0:
tsv2vcf.h: In function =91tsv_next=92:
tsv2vcf.h:68:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
tsv2vcf.h:71:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0 ^
tsv2vcf.h:73:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0 ^
vcfconvert.c: In function =91tsv_setter_chrom_pos_ref_alt=92:
vcfconvert.c:161:5: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0 while ( se < tsv->se && *se!=3D'_' && isspace(*tsv->se) ) se++;
=A0=A0=A0=A0 ^
vcfconvert.c:162:5: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0 if ( se < tsv->se && *se!=3D'_' && isspace(*tsv->se) ) error("=
Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
=A0=A0=A0=A0 ^
vcfconvert.c: In function =91tsv_setter_verify_ref_alt=92:
vcfconvert.c:195:5: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0 ^
vcfconvert.c:197:5: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0 ^
vcfconvert.c: In function =91gensample_to_vcf=92:
vcfconvert.c:354:5: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0 while ( *se && !isspace(*se) ) se++;
=A0=A0=A0=A0 ^
vcfconvert.c:378:9: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 se =3D samples[i]; while ( *se && !isspace(*se) ) =
se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfconvert.c: In function =91haplegendsample_to_vcf=92:
vcfconvert.c:502:9: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 se =3D samples[i]; while ( *se && !isspace(*se) ) =
se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfconvert.c: In function =91hapsample_to_vcf=92:
vcfconvert.c:615:9: warning: array subscript has type =91char=92 [-Wchar-su=
bscripts]
=A0=A0=A0=A0=A0=A0=A0=A0 se =3D samples[i]; while ( *se && !isspace(*se) ) =
se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfconvert.c: In function =91tsv_setter_aa1=92:
vcfconvert.c:1069:5: warning: array subscript has type =91char=92 [-Wchar-s=
ubscripts]
=A0=A0=A0=A0 int a0 =3D acgt_to_5(toupper(ss[0]));
=A0=A0=A0=A0 ^
vcfconvert.c:1070:5: warning: array subscript has type =91char=92 [-Wchar-s=
ubscripts]
=A0=A0=A0=A0 int a1 =3D ss[1] ? acgt_to_5(toupper(ss[1])) : a0;
=A0=A0=A0=A0 ^
vcfconvert.c: In function =91tsv_setter_aa=92:
vcfconvert.c:1094:5: warning: array subscript has type =91char=92 [-Wchar-s=
ubscripts]
=A0=A0=A0=A0 ref[0] =3D toupper(ref[0]);
=A0=A0=A0=A0 ^
vcfconvert.c: In function =91main_vcfconvert=92:
vcfconvert.c:1436:13: warning: implicit declaration of function =91fileno=
=92 [-Wimplicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) =
args->infname =3D "-";
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o tsv2vcf.o tsv2vcf.c
In file included from tsv2vcf.c:27:0:
tsv2vcf.h: In function =91tsv_next=92:
tsv2vcf.h:68:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
tsv2vcf.h:71:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0 ^
tsv2vcf.h:73:5: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0 ^
tsv2vcf.c: In function =91tsv_parse=92:
tsv2vcf.c:81:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && !isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
tsv2vcf.c:88:9: warning: array subscript has type =91char=92 [-Wchar-subscr=
ipts]
=A0=A0=A0=A0=A0=A0=A0=A0 while ( *tsv->se && isspace(*tsv->se) ) tsv->se++;
=A0=A0=A0=A0=A0=A0=A0=A0 ^
gcc -g -Wall -Wc++-compat -O2=A0 -std=3Dc99 -I. -Ihtslib-1.3 -DPLUGINPATH=
=3D\"/usr/local/libexec/bcftools\"=A0 -c -o vcfcnv.o vcfcnv.c
vcfcnv.c: In function =91norm_prob=92:
vcfcnv.c:602:93: error: =91M_PI=92 undeclared (first use in this function)
=A0=A0=A0=A0 return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev=
2) / param->norm / sqrt(2*M_PI*param->dev2);
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcnv.c:602:93: note: each undeclared identifier is reported only once for=
 each function it appears in
vcfcnv.c: In function =91main_vcfcnv=92:
vcfcnv.c:1349:9: warning: implicit declaration of function =91fileno=92 [-W=
implicit-function-declaration]
=A0=A0=A0=A0=A0=A0=A0=A0 if ( !isatty(fileno((FILE *)stdin)) ) fname =3D "-=
";
=A0=A0=A0=A0=A0=A0=A0=A0 ^
vcfcnv.c: In function =91norm_prob=92:
vcfcnv.c:603:1: warning: control reaches end of non-void function [-Wreturn=
-type]
=A0}
=A0^

With this final error message

Makefile:103: recipe for target 'vcfcnv.o' failed
make: *** [vcfcnv.o] Error 1



=A0Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surn=
ame and ISOGG=A0YTree=20=09=09=20=09=20=20=20=09=09=20=20
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