[med-svn] [codonw] 01/01: rename links to codonw-*
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Fri Nov 27 22:18:01 UTC 2015
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository codonw.
commit 830ba33f348d29e89d17c8fe3b0dece2cbd7cb30
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Fri Nov 27 22:16:55 2015 +0000
rename links to codonw-*
---
debian/links | 36 +--
debian/make_man.pl | 6 +-
debian/patches/fix_link_name_clashes | 515 +++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
4 files changed, 537 insertions(+), 21 deletions(-)
diff --git a/debian/links b/debian/links
index bba9228..7c555df 100644
--- a/debian/links
+++ b/debian/links
@@ -1,18 +1,18 @@
-/usr/bin/codonw /usr/bin/rscu
-/usr/bin/codonw /usr/bin/cu
-/usr/bin/codonw /usr/bin/aau
-/usr/bin/codonw /usr/bin/raau
-/usr/bin/codonw /usr/bin/tidy
-/usr/bin/codonw /usr/bin/reader
-/usr/bin/codonw /usr/bin/cutab
-/usr/bin/codonw /usr/bin/cutot
-/usr/bin/codonw /usr/bin/transl
-/usr/bin/codonw /usr/bin/bases
-/usr/bin/codonw /usr/bin/base3s
-/usr/bin/codonw /usr/bin/dinuc
-/usr/bin/codonw /usr/bin/cai
-/usr/bin/codonw /usr/bin/fop
-/usr/bin/codonw /usr/bin/gc3s
-/usr/bin/codonw /usr/bin/gc
-/usr/bin/codonw /usr/bin/cbi
-/usr/bin/codonw /usr/bin/enc
\ No newline at end of file
+/usr/bin/codonw /usr/bin/codonw-rscu
+/usr/bin/codonw /usr/bin/codonw-cu
+/usr/bin/codonw /usr/bin/codonw-aau
+/usr/bin/codonw /usr/bin/codonw-raau
+/usr/bin/codonw /usr/bin/codonw-tidy
+/usr/bin/codonw /usr/bin/codonw-reader
+/usr/bin/codonw /usr/bin/codonw-cutab
+/usr/bin/codonw /usr/bin/codonw-cutot
+/usr/bin/codonw /usr/bin/codonw-transl
+/usr/bin/codonw /usr/bin/codonw-bases
+/usr/bin/codonw /usr/bin/codonw-base3s
+/usr/bin/codonw /usr/bin/codonw-dinuc
+/usr/bin/codonw /usr/bin/codonw-cai
+/usr/bin/codonw /usr/bin/codonw-fop
+/usr/bin/codonw /usr/bin/codonw-gc3s
+/usr/bin/codonw /usr/bin/codonw-gc
+/usr/bin/codonw /usr/bin/codonw-cbi
+/usr/bin/codonw /usr/bin/codonw-enc
\ No newline at end of file
diff --git a/debian/make_man.pl b/debian/make_man.pl
index fc7da21..fc2b0fa 100755
--- a/debian/make_man.pl
+++ b/debian/make_man.pl
@@ -31,9 +31,9 @@ foreach my $tool (keys %tools) {
my $tmpl = $string;
my $uctool = uc $tool;
print @{$tools{$tool}}[0] . "\n";
- open(my $fh, '>', "$ARGV[1]/$tool.1") or die "Could not open output file $!";
- $tmpl =~ s/%%TOOLNAME%%/$tool/g;
- $tmpl =~ s/%%CTOOLNAME%%/$uctool/g;
+ open(my $fh, '>', "$ARGV[1]/codonw-$tool.1") or die "Could not open output file $!";
+ $tmpl =~ s/%%TOOLNAME%%/codonw-$tool/g;
+ $tmpl =~ s/%%CTOOLNAME%%/CODONW-$uctool/g;
$tmpl =~ s/%%TOOLDESC%%/@{$tools{$tool}}[0]/g;
$tmpl =~ s/%%TOOLOPT%%/@{$tools{$tool}}[1]/g;
print $fh "$tmpl";
diff --git a/debian/patches/fix_link_name_clashes b/debian/patches/fix_link_name_clashes
new file mode 100644
index 0000000..ea1d3ad
--- /dev/null
+++ b/debian/patches/fix_link_name_clashes
@@ -0,0 +1,515 @@
+Description: Fix_link_name_clashes
+--- a/commline.c
++++ b/commline.c
+@@ -35,16 +35,16 @@
+ /* reported to the user, arguments not preceded by a dash are assumed to */
+ /* be filenames. The input, output and bulk output files to be precise */
+ /**************************************************************************/
+-int proc_comm_line( int *pargc , char ***pargv)
++int proc_comm_line( int *pargc , char ***pargv)
+ {
+ char *p;
+ char c;
+ int n;
+ char prog_name[64];
+ char root[MAX_FILENAME_LEN];
+-
++
+ /* decide how to process argc[0] which will be the name of the programme */
+-#if defined (_WINDOWS) || defined (_DOS) || defined ( WIN32 )
++#if defined (_WINDOWS) || defined (_DOS) || defined ( WIN32 )
+ if ( (p = strrchr(**pargv, '\\')) != NULL )
+ strncpy(prog_name, p+1 , 63);
+ else
+@@ -53,26 +53,26 @@
+ if ( (p = strrchr(**pargv, '/')) != NULL )
+ strncpy(prog_name, p+1, 63);
+ else
+- strncpy(prog_name, **pargv, 10);
++ strncpy(prog_name, **pargv, 10);
+ #elif defined(VMS) || defined (OPENVMS) /* maybe VMS or OPENVMS */
+ if ( (p = strrchr(**pargv, ']')) != NULL )
+ strncpy(prog_name, p+1, 63);
+ else
+- strncpy(prog_name, **pargv, 10);
++ strncpy(prog_name, **pargv, 10);
+ #else
+ printf("UNRECOGNISED SYSTEM type won't be able to impersonate other programmes\n");
+ strcpy(prog_name, "codon"); /* OK I give up */
+ #endif
+
+- if ( (p = strrchr(prog_name, '.')) != NULL ) /* remove file extension */
++ if ( (p = strrchr(prog_name, '.')) != NULL ) /* remove file extension */
+ *p = '\0'; /* tidy.exe -> tidy */
+
+ /* first call to garg initialises the function with the command line*/
+ /* parameters and the number of arguments, subsequent calls strip */
+ /* these off one by one */
+-
++
+ /* has the user asked for help ???????????? */
+- if ((p = garg(*pargc, *pargv, "-h", GARG_EXACT)) ||
++ if ((p = garg(*pargc, *pargv, "-h", GARG_EXACT)) ||
+ (p = garg(0, NULL, "-help", GARG_EXACT))){
+ printf(
+ "codonW [inputfile] [outputfile] [bulkoutfile] [options]\n"
+@@ -80,7 +80,7 @@
+ " -h(elp)\tThis help message\n"
+ " -nomenu\tPrevent the menu interface being displayed\n"
+ " -nowarn\tPrevent warnings about sequences being displayed\n"
+- " -silent\tOverwrite files silently\n"
++ " -silent\tOverwrite files silently\n"
+ " -totals\tConcatenate all genes in inputfile\n"
+ " -machine\tMachine readable output\n"
+ " -human\t\tHuman readable output\n"
+@@ -100,6 +100,7 @@
+ "positions\n"
+
+ );
++ pause;
+ printf(
+ " -L_sym\t\tNumber of synonymous codons\n"
+ " -L_aa\t\tTotal number of synonymous and non-synonymous codons\n"
+@@ -123,6 +124,7 @@
+ " -raau\t\tRelative Amino Acid Usage (RAAU)\n"
+ " -cu\t\tCodon Usage (CU) (default)\n"
+ );
++ pause;
+ printf(
+ " -cutab\t\tTabulation of codon usage\n"
+ " -cutot\t\tTabulation of dataset's codon usage\n"
+@@ -137,37 +139,38 @@
+ "\nWhere {file} represents an input filename, and N an integer"
+ " value"
+ );
++ pause;
+ my_exit(99,""); /* after writing out help quit */
+ }
+-
+
+-/* These parameters are normally set in menu3 ie. the defaults menu */
++
++/* These parameters are normally set in menu3 ie. the defaults menu */
+ /* for a explanation of the various GARG_FLAGS see gargs */
+
+ /* -silent stops warnings about file about to be overwritten */
+- if (garg(0, NULL, "-silent", GARG_THERE))
++ if (garg(0, NULL, "-silent", GARG_THERE))
+ pm->verbose = FALSE;
+
+-
++
+ /* -total causes sequences to be concatenated and treated as one sequence */
+ if ( garg(0, NULL, "-total" , GARG_THERE))
+- pm->totals = TRUE;
++ pm->totals = TRUE;
+
+ /* -machine or -human determines for whom the output should be formatted */
+- if (p = garg(0, NULL, "-human", GARG_THERE))
++ if (p = garg(0, NULL, "-human", GARG_THERE))
+ pm->seq_format = 'H';
+ if (p = garg(0, NULL, "-mach", GARG_THERE))
+ pm->seq_format = 'M';
+
+-/* -code determines the genetic code */
++/* -code determines the genetic code */
+ if (p = garg(0, NULL, "-code", GARG_NEXT | GARG_EXACT)) {
+ strcpy(pm->junk, p);
+ n=0;
+- while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
++ while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
+ n++;
+ if ( n != (int)strlen(pm->junk)
+- || atoi(pm->junk) < 0 || atoi(pm->junk) > NumGeneticCodes ) {
+- printf( "FATAL: The value for genetic code %s is invalid\n",
++ || atoi(pm->junk) < 0 || atoi(pm->junk) > NumGeneticCodes ) {
++ printf( "FATAL: The value for genetic code %s is invalid\n",
+ pm->junk);
+ my_exit(99,"Fatal error in genetic code value");
+ } else {
+@@ -184,14 +187,14 @@
+ if (p = garg(0, NULL, "-f_type", GARG_NEXT | GARG_EXACT)) {
+ strcpy(pm->junk, p);
+ n = 0;
+- while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
++ while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
+ n++;
+- if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
++ if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
+ atoi(pm->junk) >= NumFopSpecies ) {
+- printf("FATAL: The value for fop_type %s is not valid\n",
++ printf("FATAL: The value for fop_type %s is not valid\n",
+ pm->junk);
+ my_exit(99,"Fatal error in Fop value");
+- } else {
++ } else {
+ pm->f_type = (char) atoi(p); /* define organism type for Fop */
+ initilize_point(pm->code, pm->f_type, pm->c_type);
+ }
+@@ -203,11 +206,11 @@
+ if (p = garg(0, NULL, "-c_type", GARG_NEXT | GARG_EXACT)) {
+ strcpy(pm->junk,p);
+ n = 0;
+- while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
++ while ( isdigit( (int) pm->junk[n]) && pm->junk[n] != '\0')
+ n++;
+- if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
++ if ( n != (int)strlen(pm->junk) || atoi(pm->junk) < 0 ||
+ atoi(pm->junk) >= NumCaiSpecies) {
+- printf("FATAL: The value for cai_type %s is not valid\n",
++ printf("FATAL: The value for cai_type %s is not valid\n",
+ pm->junk);
+ my_exit(99,"Fatal error in CAI type value");
+
+@@ -244,7 +247,7 @@
+ if (p = garg(0, NULL, "-hyd" , GARG_EXACT))
+ pm->hyd = TRUE;
+ if (p = garg(0, NULL, "-aro" , GARG_EXACT))
+- pm->aro = TRUE;
++ pm->aro = TRUE;
+ /* Turns on all the above indices */
+ if (p = garg(0, NULL, "-all_indices" , GARG_EXACT)){
+ pm->cai = TRUE;
+@@ -257,23 +260,23 @@
+ pm->L_sym = TRUE;
+ pm->L_aa = TRUE;
+ pm->hyd = TRUE;
+- pm->aro = TRUE;
++ pm->aro = TRUE;
+ }
+
+ /* This section in used to input the filenames for personal choices of Fop */
+ /* CBI or CAI values. The name is tested to make sure the file is readable */
+ /* the pointer to the file is then assign to the relevant pointer in the */
+ /* struct Z_menu and then processed properly in codon_us.c */
+-
+-/* Fop */
++
++/* Fop */
+ if (p = garg(0, NULL, "-fop_file", GARG_NEXT | GARG_EXACT)) {
+ if ( (pm->fopfile = open_file( "", p, "r", FALSE)) == NULL ) {
+ printf("Could not open Fop file - %s\n", p);
+ my_exit(1,"commline open fop file");
+ } else
+- strncpy(pm->fop_filen, pm->junk, MAX_FILENAME_LEN - 1);
++ strncpy(pm->fop_filen, pm->junk, MAX_FILENAME_LEN - 1);
+ /* idiot catch, if you load personal fop values you want to calculate fop */
+- pm->fop=TRUE;
++ pm->fop=TRUE;
+ }
+
+ /* CAI */
+@@ -307,15 +310,15 @@
+ pm->coa = 'a';
+ if (p = garg(0, NULL, "-coa_expert", GARG_EXACT)) /* detailed inertia */
+ (coa.level='e'); /* analysis */
+-
+-
++
++
+ /* These are options selectable under the advanced COA menu */
+-/* This first option -coa_axes changes the number of axis recorded to file */
++/* This first option -coa_axes changes the number of axis recorded to file */
+ if (p = garg(0, NULL, "-coa_axes", GARG_NEXT | GARG_EXACT)){
+- if ( isdigit( (int) *p) ){
+- n = (char)atoi(p);
+- /* just check that correspondence analysis has been selected */
+- if ( pm->coa == 'a' && (n > 20 || n<0) || ( n<0 || n>59 )) {
++ if ( isdigit( (int) *p) ){
++ n = (char)atoi(p);
++ /* just check that correspondence analysis has been selected */
++ if ( pm->coa == 'a' && (n > 20 || n<0) || ( n<0 || n>59 )) {
+ fprintf(pm->my_err,"Value %d is out of range for Number COA Axis "
+ "adjusting to max value\n",n);
+ if ( pm->coa == 'a' ) pcoa->axis = 20; else pcoa->axis = 59;
+@@ -324,7 +327,7 @@
+ }
+ }
+ }
+-
++
+ /* Select the size of dataset to use to identify optimal codons */
+ if (p = garg(0, NULL, "-coa_num", GARG_NEXT|GARG_EXACT)) {
+ strcpy (pm->junk,p) ;
+@@ -333,8 +336,8 @@
+ pcoa->fop_gene=atoi(pm->junk)*-1;
+ }else {
+ pcoa->fop_gene=atoi(pm->junk);
+- }
+- }
++ }
++ }
+
+
+ /* These option are mutually exclusive and are normally selected using the */
+@@ -349,7 +352,7 @@
+ if ( p = garg(0, NULL, "-cutot", GARG_THERE)){
+ pm->bulk = 'C';
+ pm->totals =TRUE;
+- }
++ }
+ if ( p = garg(0, NULL, "-reader", GARG_EXACT))
+ pm->bulk = 'R';
+ if ( p = garg(0, NULL, "-rscu", GARG_EXACT))
+@@ -362,16 +365,16 @@
+ pm->bulk = 'A';
+ if ( p = garg(0, NULL, "-transl", GARG_THERE))
+ pm->bulk = 'N';
+- if ( p = garg(0, NULL, "-base", GARG_THERE))
++ if ( p = garg(0, NULL, "-base", GARG_THERE))
+ pm->bulk = 'B';
+ if (p = garg(0, NULL, "-dinuc", GARG_THERE))
+ pm->bulk = 'D';
+ if (p = garg(0, NULL, "-noblk", GARG_EXACT))
+ pm->bulk = 'X';
+-
++
+ /* -t is used to change the column separator used in the output files */
+ /* at present it must be a space, tab or comma */
+-/* Must occur after -transl or it misreads transl as a seperator */
++/* Must occur after -transl or it misreads transl as a seperator */
+ if (p = garg(0, NULL, "-t" , GARG_NEXT | GARG_SUBSQ)) {
+ strcpy(pm->junk, p);
+ n = 0;
+@@ -382,11 +385,11 @@
+ printf( "WARNING: The chosen separator %s is unsuitable use"
+ "comma, tab or space\n", pm->junk);
+ } else {
+- pm->seperator = c;
++ pm->seperator = c;
+ }
+ }
+-
+-
++
++
+ /* These options are commandline specific, ie. they do not have an */
+ /* menu option */
+
+@@ -417,67 +420,67 @@
+ /* programmes. In essence CodonW will impersonate other commonly used */
+ /* codon usage analysis programmes if called using a special name */
+
+- if ( !strcmp(prog_name, "raau" ) )
++ if ( !strcmp(prog_name, "raau") || !strcmp(prog_name+7, "raau"))
+ pm->bulk = 'L';
+- else if ( !strcmp(prog_name, "cu" ) )
++ else if ( !strcmp(prog_name, "cu") || !strcmp(prog_name+7, "cu"))
+ pm->bulk = 'C';
+- else if ( !strcmp(prog_name, "cutab" ) )
++ else if ( !strcmp(prog_name, "cutab") || !strcmp(prog_name+7, "cutab"))
+ pm->bulk = 'O';
+- else if ( !strcmp(prog_name, "reader") )
++ else if ( !strcmp(prog_name, "reader") || !strcmp(prog_name+7, "reader"))
+ pm->bulk = 'R';
+- else if ( !strcmp(prog_name, "rscu" ) )
++ else if ( !strcmp(prog_name, "rscu") || !strcmp(prog_name+7, "rscu"))
+ pm->bulk = 'S';
+- else if ( !strcmp(prog_name, "tidy" ) )
++ else if ( !strcmp(prog_name, "tidy") || !strcmp(prog_name+7, "tidy"))
+ pm->bulk = 'T';
+- else if ( !strcmp(prog_name, "aau" ) )
++ else if ( !strcmp(prog_name, "aau") || !strcmp(prog_name+7, "aau"))
+ pm->bulk = 'A';
+- else if ( !strcmp(prog_name, "dinuc" ) )
++ else if ( !strcmp(prog_name, "dinuc") || !strcmp(prog_name+7, "dinuc"))
+ pm->bulk = 'D';
+- else if ( !strcmp(prog_name, "transl") )
++ else if ( !strcmp(prog_name, "transl") || !strcmp(prog_name+7, "transl"))
+ pm->bulk = 'N';
+- else if ( !strcmp(prog_name, "bases" ) )
+- pm->bulk = 'B';
+- else if ( !strcmp(prog_name, "base3s") ) {
++ else if ( !strcmp(prog_name, "bases") || !strcmp(prog_name+7, "bases"))
++ pm->bulk = 'B';
++ else if ( !strcmp(prog_name, "base3s") || !strcmp(prog_name+7, "base3s")) {
+ pm->prog = 's' ;
+ pm->menu = FALSE;
+ pm->sil_base = TRUE;
+- } else if ( !strcmp(prog_name, "cai" ) ) {
++ } else if ( !strcmp(prog_name, "cai") || !strcmp(prog_name+7, "cai")) {
+ pm->prog = 'c';
+ pm->menu = FALSE;
+ pm->cai = TRUE;
+- } else if ( !strcmp(prog_name, "fop" ) ) {
++ } else if ( !strcmp(prog_name, "fop") || !strcmp(prog_name+7, "fop")) {
+ pm->prog = 'f';
+ pm->menu = FALSE;
+ pm->fop = TRUE;
+- } else if ( !strcmp(prog_name, "gc3s" ) ) {
++ } else if ( !strcmp(prog_name, "gc3s") || !strcmp(prog_name+7, "gc3s")) {
+ pm->prog = '3';
+ pm->menu = FALSE;
+ pm->gc3s = TRUE;
+- } else if ( !strcmp(prog_name, "gc" ) ) {
++ } else if ( !strcmp(prog_name, "gc") || !strcmp(prog_name+7, "gc")) {
+ pm->prog = 'g';
+ pm->menu = FALSE;
+ pm->gc = TRUE;
+- } else if ( !strcmp(prog_name, "enc" ) ) {
++ } else if ( !strcmp(prog_name, "enc") || !strcmp(prog_name+7, "enc")) {
+ pm->prog = 'e';
+ pm->menu = FALSE;
+ pm->enc = TRUE;
+- } else if ( !strcmp(prog_name, "cbi" ) ) {
++ } else if ( !strcmp(prog_name, "cbi") || !strcmp(prog_name+7, "cbi")) {
+ pm->prog = 'i';
+ pm->menu = FALSE;
+ pm->cbi = TRUE;
+- } else if ( !strcmp(prog_name, "cutot" ) ) {
++ } else if ( !strcmp(prog_name, "cutot") || !strcmp(prog_name+7, "cutot")) {
+ pm->bulk = 'C';
+ pm->menu = FALSE;
+ pm->totals =TRUE;
+ } else {
+ pm->codonW=TRUE; /* if argc[0] is not recognised assume codons*/
+ /* if blk output is still X then assume cu */
+- if (pm->bulk=='X') pm->bulk='C';
++ if (pm->bulk=='X') pm->bulk='C';
+ }
+
+
+ if (!pm->codonW ) { /* we appear to be impersonating another prog*/
+- /* now we switch to the correct greeting */
++ /* now we switch to the correct greeting */
+ if (pm->bulk && pm->bulk!='X'){
+ pm->seperator='\000'; /* stop chars being converted by tidy*/
+ switch (pm->bulk) {
+@@ -564,7 +567,7 @@
+ /* so now we test for any remaining, these are unrecognised */
+
+ while (p = garg(0, NULL, "-", GARG_THERE))
+- if ( pm->menu )
++ if ( pm->menu )
+ printf("Unrecognised argument %s\n", p);
+ else {
+ /* if we are running without a menu then abort this run */
+@@ -584,24 +587,24 @@
+ }
+ /* The second should be the output filename */
+ if ( p = garg(0, NULL, "", GARG_THERE)) {
+- if ( (pm->outputfile = open_file( "", p, "w",
++ if ( (pm->outputfile = open_file( "", p, "w",
+ (int) pm->verbose)) == NULL ) {
+ printf("Could not open output file - %s\n", p );
+ my_exit(1,"commline out file");
+ } else
+ strncpy(pm->curr_outfilename, pm->junk, MAX_FILENAME_LEN - 1);
+- }
++ }
+
+ /* The third which only occurs if the programme is running as CodonW */
+
+ if ( pm->codonW && (p = garg(0, NULL, "", GARG_THERE)) ) {
+- if ( (pm->tidyoutfile = open_file( "", p, "w",
++ if ( (pm->tidyoutfile = open_file( "", p, "w",
+ (int) pm->verbose)) == NULL ) {
+ printf("Could not open blkoutput file - %s\n", p );
+ my_exit(1,"commline blk outfile");
+ } else
+ strncpy(pm->curr_tidyoutname, pm->junk, MAX_FILENAME_LEN - 1);
+- }
++ }
+
+ /* Now check the command line is empty ... it should be at this point */
+ while (p = garg(0, NULL, "", GARG_THERE))
+@@ -612,25 +615,25 @@
+ /* we need to load an input file name */
+
+ if ( (!pm->codonW || !pm->menu) && !pm->inputfile ){
+- if ( (pm->inputfile = open_file( "input filename", "input.dat",
++ if ( (pm->inputfile = open_file( "input filename", "input.dat",
+ "r", FALSE)) == NULL ) {
+ printf("Could not open input file - %s\n", p );
+ my_exit(1,"commline inputfile");
+- }
++ }
+ strncpy(pm->curr_infilename, pm->junk, MAX_FILENAME_LEN - 1);
+ }
+-
++
+ /* If we have an input filename but no output then we must prompt for the */
+ /* output filename */
+
+- if ( pm->inputfile && !pm->outputfile ) {
++ if ( pm->inputfile && !pm->outputfile ) {
+ /* If we are trying to impersonate another programme use this method*/
+ /* but make sure that we know what this other programme is called */
+ if ( !pm->codonW && strlen (prog_name) ){
+ strcpy(pm->curr_outfilename, prog_name);
+ strcat(pm->curr_outfilename, ".def");
+ } else {
+-
++
+ /* Use the input filename as a root filename */
+ strncpy(root, pm->curr_infilename, MAX_FILENAME_LEN - 5);
+ for (n = (int) strlen(root); n && root[n]!='.' ; --n);
+@@ -638,23 +641,23 @@
+
+ strcpy(pm->curr_outfilename, root);
+ strcat(pm->curr_outfilename, ".out");
+- } /* matchs else */
++ } /* matchs else */
+
+- /* now we know the suggested name for the output file lets open it */
++ /* now we know the suggested name for the output file lets open it */
+ if ( pm->verbose ) {
+ if ( (pm->outputfile = open_file( "indices output filename",
+- pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
++ pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
+ my_exit(1,"commline");
+ strncpy(pm->curr_outfilename, pm->junk, MAX_FILENAME_LEN - 1);
+ }else{
+ if ( (pm->outputfile = open_file( "",
+- pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
++ pm->curr_outfilename, "w",(int) pm->verbose)) == NULL )
+ my_exit(1,"commline");
+ strncpy(pm->curr_outfilename, pm->junk, MAX_FILENAME_LEN - 1);
+ }
+
+ } /* match if ( pm->inputfile */
+-
++
+
+
+ /* we had a commandline inputfile name and output filename but none */
+@@ -670,22 +673,22 @@
+ strcpy(pm->curr_tidyoutname, root);
+ strcat(pm->curr_tidyoutname, ".blk");
+
+- /* now we know the suggested name for the output file lets open it */
++ /* now we know the suggested name for the output file lets open it */
+ if( pm->verbose) {
+ if ( (pm->tidyoutfile = open_file( "bulk output filename",
+- pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
++ pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
+ my_exit(1,"commline");
+ strncpy(pm->curr_tidyoutname, pm->junk, MAX_FILENAME_LEN - 1);
+ }else{
+ if ( (pm->tidyoutfile = open_file( "",
+- pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
++ pm->curr_tidyoutname, "w",(int) pm->verbose)) == NULL )
+ my_exit(1,"commline");
+ strncpy(pm->curr_tidyoutname, pm->junk, MAX_FILENAME_LEN - 1);
+ }
+- }else{
++ }else{
+ /* only use one output file when impersonating other programmes */
+- /* just in case we make blkout and output the same file */
+- pm->tidyoutfile = pm->outputfile;
++ /* just in case we make blkout and output the same file */
++ pm->tidyoutfile = pm->outputfile;
+ }
+ }
+ return 1;
+@@ -699,8 +702,8 @@
+ /* This subroutine was developed as a collaboration with Colin McFarlane */
+ /* GARG_EXACT The argument must match targ exactly */
+ /* GARG_THERE The targ may be sub-string of the argument */
+-/* GARG_SUBSQ The string immediate after targ is returned */
+-/* GARG_NEXT The next argument after targ is returned */
++/* GARG_SUBSQ The string immediate after targ is returned */
++/* GARG_NEXT The next argument after targ is returned */
+ /* else return NULL */
+ /***************************************************************************/
+ char *garg(int argc, char *argv[], const char *targ, int mode)
diff --git a/debian/patches/series b/debian/patches/series
index 88a3e40..0025e5f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ remove_pause
define_linux
spelling
helpfile_location
+fix_link_name_clashes
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/codonw.git
More information about the debian-med-commit
mailing list