[med-svn] [Git][med-team/coils][master] 2 commits: Fix function prototype in coils-wrap patch (Closes: #1096450)
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat Sep 20 15:01:26 BST 2025
Nilesh Patra pushed to branch master at Debian Med / coils
Commits:
cdc87784 by Nilesh Patra at 2025-09-20T19:28:00+05:30
Fix function prototype in coils-wrap patch (Closes: #1096450)
- - - - -
fa204f85 by Nilesh Patra at 2025-09-20T19:28:28+05:30
Upload to unstable
- - - - -
2 changed files:
- debian/changelog
- debian/patches/coils-wrap
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+coils (2002-10) unstable; urgency=medium
+
+ * Team Upload.
+ * Fix function prototype in coils-wrap patch (Closes: #1096450)
+
+ -- Nilesh Patra <nilesh at debian.org> Sat, 20 Sep 2025 19:28:06 +0530
+
coils (2002-9) unstable; urgency=medium
* Team Upload.
=====================================
debian/patches/coils-wrap
=====================================
@@ -22,7 +22,7 @@ Description:
# Runs coils multiply to give you a three-window output
-@@ -9,42 +11,75 @@ $|=1;
+@@ -9,42 +11,75 @@
# You may need to change these, in addition
# to the "/usr/local/bin/perl" above if necessary
#
@@ -117,7 +117,7 @@ Description:
if($type ne "f") {
die "Error file must be in FASTA format\n";
}
-@@ -61,14 +96,14 @@ $seqfile = $tmpdir . "coils." . $$ . ".f
+@@ -61,14 +96,14 @@
$seqs = get_afasta(@data);
@@ -139,7 +139,7 @@ Description:
for($n=0; $n<$seqs->{nseq}; ++$n) {
$id = $seqs->{list}[$n];
$in_seq = $seqs->{ids}{$id}{seq};
-@@ -76,7 +111,8 @@ for($n=0; $n<$seqs->{nseq}; ++$n) {
+@@ -76,7 +111,8 @@
# print "ID $id seq $seq\n";
&write_fasta($seqfile,$id,$in_seq);
@@ -149,7 +149,7 @@ Description:
if($mode eq "threewin") {
# Runs threewin style mode
# Three windows 14,21,28
-@@ -94,7 +130,10 @@ for($n=0; $n<$seqs->{nseq}; ++$n) {
+@@ -94,7 +130,10 @@
for($i=14; $i<=28; $i+=7) {
$j=($i-14)/7;
$command = $coils_exec . $extra . " -win " . $i . " < " . $seqfile;
@@ -161,7 +161,7 @@ Description:
open(IN,"$command|");
$fid = "frame-" . $i;
-@@ -107,7 +146,18 @@ for($n=0; $n<$seqs->{nseq}; ++$n) {
+@@ -107,7 +146,18 @@
$p=0;
while(<IN>) {
@@ -181,7 +181,7 @@ Description:
$_ =~ s/^ *//;
@t=split(/ +/);
$align->{ids}{$fid}{seq} .= $t[2];
-@@ -118,18 +168,22 @@ for($n=0; $n<$seqs->{nseq}; ++$n) {
+@@ -118,18 +168,22 @@
else { $sP = substr($P,0,1); }
if($sP eq "0") { $sP = "-"; }
$align->{ids}{$pid}{seq} .= $sP;
@@ -211,7 +211,7 @@ Description:
sub write_fasta {
my($fn,$id,$seq) = @_;
-@@ -139,7 +193,7 @@ sub write_fasta {
+@@ -139,7 +193,7 @@
while($i<length($seq)) {
$aa = substr($seq,$i,1);
print SEQ $aa;
@@ -220,7 +220,7 @@ Description:
$i++;
}
print SEQ "\n";
-@@ -150,12 +204,14 @@ sub write_clustal {
+@@ -150,12 +204,14 @@
my($align) = $_[0];
my($i,$j,$k,$id);
@@ -238,7 +238,7 @@ Description:
foreach $id (keys %{$align->{ids}}) {
if(defined($align->{ids}{$id}{start})) {
-@@ -164,24 +220,44 @@ sub write_clustal {
+@@ -164,24 +220,44 @@
$align->{ids}{$id}{newid} .= $align->{ids}{$id}{ranges};
}
} else {
@@ -300,7 +300,7 @@ Description:
}
sub get_afasta {
-@@ -222,7 +298,7 @@ sub get_afasta {
+@@ -222,7 +298,7 @@
if(defined($align->{ids}{$label})) {
$_ =~ s/-/ /g;
$align->{ids}{$label}{seq} .= $_;
@@ -309,7 +309,7 @@ Description:
}
}
}
-@@ -233,6 +309,7 @@ sub get_afasta {
+@@ -233,6 +309,7 @@
}
sub read_align { # Just read in text and modify format if necessary
@@ -317,7 +317,7 @@ Description:
#
# Likely format is determined by looking for signs of one format over another
-@@ -255,7 +332,7 @@ sub read_align { # Just read in text and
+@@ -255,7 +332,7 @@
my($file) = $_[0];
my(@data);
my($i,$type);
@@ -326,7 +326,7 @@ Description:
@data=();
-@@ -268,18 +345,19 @@ sub read_align { # Just read in text and
+@@ -268,18 +345,19 @@
for($i=0; $i<=$#data; ++$i) {
$_ = $data[$i];
@@ -349,7 +349,7 @@ Description:
}
# Block and FASTA are quite hard to tell apart in a quick parse,
-@@ -289,14 +367,12 @@ sub read_align { # Just read in text and
+@@ -289,14 +367,12 @@
if($block_end==0) { $votes{"f"}++; }
}
@@ -366,7 +366,7 @@ Description:
return @data;
}
sub get_print_string {
-@@ -311,3 +387,5 @@ sub get_print_string {
+@@ -311,3 +387,5 @@
}
return $max_len;
}
@@ -403,7 +403,7 @@ Description:
int mode;
int min_seg;
-@@ -39,7 +43,8 @@ main(int argc, char *argv[]) {
+@@ -39,7 +43,8 @@
char heptfile[HEPTFILELENGTH];
char *buff;
static char *env;
@@ -413,7 +413,7 @@ Description:
float min_P;
-@@ -55,10 +60,10 @@ main(int argc, char *argv[]) {
+@@ -55,10 +60,10 @@
mode = 0; /* 0 = column mode, 1 = fasta, 2 = concise */
min_P = 0.5;
@@ -427,7 +427,7 @@ Description:
exit(-1);
}
-@@ -67,19 +72,19 @@ main(int argc, char *argv[]) {
+@@ -67,19 +72,19 @@
for(i=1; i<argc; ++i) {
@@ -451,7 +451,7 @@ Description:
sscanf(argv[i+1],"%d",&min_seg);
i++;
} else if(strcmp(&argv[i][1],"c")==0) {
-@@ -87,18 +92,18 @@ main(int argc, char *argv[]) {
+@@ -87,18 +92,18 @@
} else if((strcmp(&argv[i][1],"f")==0) || (strcmp(&argv[i][1],"fasta")==0)) {
mode=1;
} else if((strcmp(&argv[i][1],"min_P")==0)) {
@@ -473,7 +473,7 @@ Description:
}
}
-@@ -175,14 +180,14 @@ main(int argc, char *argv[]) {
+@@ -175,14 +180,14 @@
pred_coils(seq,ident,title,h,window,which,weighted,mode,min_P,&t,&tc,min_seg);
free(seq);
}
@@ -490,7 +490,7 @@ Description:
fprintf(stderr,"format: ncoils [options] < [sequence file]\n");
fprintf(stderr," -f or -fasta [fasta output - coils as 'x', like '-x' in seg]\n");
fprintf(stderr," -c [concise mode - which sequences have any coils (and how many)]\n");
-@@ -191,7 +196,7 @@ void exit_error() {
+@@ -191,7 +196,7 @@
fprintf(stderr," -win <int> [window size; DEFAULT = 21]\n");
fprintf(stderr," -w [weight heptad positions a&d the same as b,c,e,f,g]\n");
fprintf(stderr," -v [verbose/debug mode - print extra junk]\n");
@@ -499,7 +499,7 @@ Description:
fprintf(stderr,"\n");
fprintf(stderr,"NCOILS, Rob Russell and Andrei Lupas, 1999\n");
fprintf(stderr," based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164\n");
-@@ -206,7 +211,6 @@ void pred_coils(char *seq,char *ident,ch
+@@ -206,7 +211,6 @@
int i,j;
int len,pos,aa_pt;
@@ -689,6 +689,14 @@ Description:
#define AAs "A_CDEFGHI_KLMN_PQRST_VW_Y_"
#define PI 3.1415
+@@ -25,6 +24,6 @@
+
+
+ struct hept_pref *read_matrix(FILE *MAT);
+-void exit_error();
++void exit_error(const char*);
+ void pred_coils(char *seq,char *ident,char *title,struct hept_pref *h,int win,int which,
+ int weighted,int fasta,float min_P, int *t, int *tc, int min_segs);
--- a/read_matrix.c
+++ b/read_matrix.c
@@ -1,4 +1,5 @@
View it on GitLab: https://salsa.debian.org/med-team/coils/-/compare/7dba2318bff9bed3c16e608b65ba50c8bd2b9347...fa204f852b31f7760565bb7be84a224f0b98e93c
--
View it on GitLab: https://salsa.debian.org/med-team/coils/-/compare/7dba2318bff9bed3c16e608b65ba50c8bd2b9347...fa204f852b31f7760565bb7be84a224f0b98e93c
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