path: root/sci-biology/consed/files/consed-29-fix-qa.patch

Fix various QA violations, due to
* implicit declarations
* incorrect printf() format specifiers
* incorrect function prototypes
* remove unsafe gets() fucntion

--- a/misc/454/sff2scf.c
+++ b/misc/454/sff2scf.c
@@ -39,6 +39,7 @@
 void writeScfFile(char *filearg, char *outfile);
 void writeScfCommand(char *filearg, char *outfile);
 
+int sffinfo(int argc, char *argv[], FILE* pTempFile );
 
 int main(int argc, char *argv[])
 {
--- a/misc/mktrace/mktrace.c
+++ b/misc/mktrace/mktrace.c
@@ -70,9 +70,9 @@
   else
   {
     printf( "enter FASTA filename: " );
-    gets( ifnm );
+    fgets( ifnm, sizeof(ifnm), stdin );
     printf( "enter output filename: " );
-    gets( ofnm );
+    fgets( ofnm, sizeof(ofnm), stdin );
   }
 
   /*
@@ -192,7 +192,7 @@
   /*
   ** Write phd file.
   */
-  if( writePhd( ofnm, numBase, seq, qual, pos, numPoint, trace ) == ERROR )
+  if( writePhd( ofnm, numBase, seq, qual, pos, numPoint ) == ERROR )
   {
     fprintf( stderr, "mktrace: error: bad status: writePhd\n" );
     free( seq );
--- a/misc/mktrace/mktrace.h
+++ b/misc/mktrace/mktrace.h
@@ -37,8 +37,8 @@
 int writeSCF( char *filename, int numBase, char *seq, int numPoint, float **trace );
 int freeTrace( float **trace );
 char *readFASTA( char *filename, char *entryName, char *comments, int *len );
-int writePhd( char *ofnm, int numBase, char *seq, int *pos, int numPoint );
 int *readQUAL( char *filename, char *entryName, char *comments, int *len );
+char *getTime( void );
 #else
 int writePhd();
 float **synTrace();
--- a/misc/phd2fasta/phd2fasta.h
+++ b/misc/phd2fasta/phd2fasta.h
@@ -276,6 +276,10 @@
                 Comments *comments, Seq *seq, TagList *tagList, char *emsg );
 int checkIntString( char *string );
 int delimiterTest( char *string, unsigned int mask );
+int checkParam( Option *option );
+char* getVersion( void );
+int showDoc( void );
+char* getTime( void );
 #else
 Option *getOption();
 struct Tag *allocTag();
--- a/misc/phd2fasta/readStdTag.c
+++ b/misc/phd2fasta/readStdTag.c
@@ -699,11 +699,11 @@
       if( fstat )
       {
         fprintf( stderr,
-                 "readStdTag: %s: line: %d: unexpected delimiter %s\n",
+                 "readStdTag: %s: line: %p: unexpected delimiter %s\n",
                   filename,
                   nline,
                   line );
-        sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n",
+        sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n",
                  filename,
                  nline,
                  line );
--- a/misc/phd2fasta/readWholeReadTag.c
+++ b/misc/phd2fasta/readWholeReadTag.c
@@ -393,11 +393,11 @@
       if( fstat )
       {
         fprintf( stderr,
-                 "readWholeReadTag: %s: line: %d: unexpected delimiter %s\n",
+                 "readWholeReadTag: %s: line: %p: unexpected delimiter %s\n",
                   filename,
                   nline,
                   line );
-        sprintf( emsg, "%s: line: %d: unexpected delimiter %s\n",
+        sprintf( emsg, "%s: line: %p: unexpected delimiter %s\n",
                  filename,
                  nline,
                  line );
--- a/misc/phd2fasta/writeFasta.c
+++ b/misc/phd2fasta/writeFasta.c
@@ -39,7 +39,7 @@
 #include "phd2fasta.h"
 
 #ifdef ANSI_C
-writeFasta( FILE *sfp, FILE *qfp, FILE *bfp,
+int writeFasta( FILE *sfp, FILE *qfp, FILE *bfp,
             int outBasePosOption,
             Comments *comments, Seq *seq, TagList *tagList, char *emsg )
 #else
--- a/motifutils.cpp
+++ b/motifutils.cpp
@@ -202,13 +202,13 @@
 void printButtonEvent( XButtonEvent* pEvent ) {
 
    printf( "type = %d\n", pEvent->type );
-   printf( "serial = %d\n", pEvent->serial );
+   printf( "serial = %lu\n", pEvent->serial );
    printf( "send_event = %s\n", szPrintBool( pEvent->send_event ) );
-   printf( "*display = %x\n", pEvent->display );
-   printf( "window = %x\n", pEvent->window );
-   printf( "root = %x\n", pEvent->root );
-   printf( "subwindow = %x\n", pEvent->subwindow );
-   printf( "time = %d\n", pEvent->time );
+   printf( "*display = %p\n", pEvent->display );
+   printf( "window = %lu\n", pEvent->window );
+   printf( "root = %lu\n", pEvent->root );
+   printf( "subwindow = %lu\n", pEvent->subwindow );
+   printf( "time = %lu\n", pEvent->time );
    printf( "x = %d\n", pEvent->x );
    printf( "y = %d\n", pEvent->y );
    printf( "x_root = %d\n", pEvent->x_root );
--- a/parseAceFile.cpp
+++ b/parseAceFile.cpp
@@ -45,6 +45,7 @@
 using namespace std;
 #include    "basesegment.h"
 #include    <stdio.h>
+#include    <stddef.h>
 #include    <string.h>
 #include    <sstream>
 #include    "mbt_errors.h"
@@ -292,7 +293,7 @@
    char* szPossibleComp = szReadName + nLength - nCOMP;
 
    if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) {
-      szPossibleComp = '\0';
+      szPossibleComp = NULL;
       return( true );
    }
    else
--- a/phaster2PhdBall.cpp
+++ b/phaster2PhdBall.cpp
@@ -547,7 +547,7 @@
 
    int nTokens = 
       sscanf( soLine_.data(), 
-              "%s %*s %d %d %lld %s %s %*s %d %d %lld %s %s\n",
+              "%s %*s %d %d %ld %s %s %*s %d %d %ld %s %s\n",
               soReadName_.data(),
               &nRead1Left_,
               &nRead1Right_,
--- a/printAutoFinishMiscInfo.cpp
+++ b/printAutoFinishMiscInfo.cpp
@@ -80,7 +80,7 @@
    int nError = stat( (char*) soAceFileFullPathname.data(), &statBuffer );
    
    if (nError == 0 ) {
-      fprintf( pAO,"size: %d date: %s\n",
+      fprintf( pAO,"size: %ld date: %s\n",
                (long) statBuffer.st_size,
                ctime( &( statBuffer.st_mtime )) );
 
--- a/printAutoFinishParameters.cpp
+++ b/printAutoFinishParameters.cpp
@@ -206,7 +206,7 @@
        pCP->nInexactSearchForStringMaxPerCentMismatch_ );
 
    fprintf( pAO, "! when using the inexact search for string, allow up to this\n");
-   fprintf( pAO, "! % mismatch:  the sum of the insertion, deletion, and substitution\n");
+   fprintf( pAO, "! %% mismatch:  the sum of the insertion, deletion, and substitution\n");
    fprintf( pAO, "! differences divided by the length of the query string\n");
    fprintf( pAO, "! (YES)\n");
    fprintf( pAO, "consed.onlyAllowOneReadWriteConsedAtATime: %s\n",
@@ -825,7 +825,7 @@
    fprintf( pAO, "! template will be 1500 bases from the forward read.  But if this template\n");
    fprintf( pAO, "! has an insert that is shorter than average, the walk may walk into vector.\n");
    fprintf( pAO, "! To be conservative, we may want to assume that the insert is somewhat \n");
-   fprintf( pAO, "! shorter than average.  By default, we assume that it is 90% as large as \n");
+   fprintf( pAO, "! shorter than average.  By default, we assume that it is 90%% as large as \n");
    fprintf( pAO, "! the average. This parameter gives that percentage.  This parameter\n");
    fprintf( pAO, "! is used both by Consed and Autofinish.\n");
    fprintf( pAO, "! (OK)\n");
@@ -1249,9 +1249,9 @@
        pCP->nAutoFinishConfidenceThatReadWillCoverSingleSubcloneRegion_ );
 
    fprintf( pAO, "! Autofinish computes the per cent of existing reads are aligned at\n");
-   fprintf( pAO, "! each base position.  Typically, this number starts at around 0% at\n");
-   fprintf( pAO, "! base position 1, rises to close to 100% at around base position 300,\n");
-   fprintf( pAO, "! and then drops again to 0% at base position 800 or so.  This number\n");
+   fprintf( pAO, "! each base position.  Typically, this number starts at around 0%% at\n");
+   fprintf( pAO, "! base position 1, rises to close to 100%% at around base position 300,\n");
+   fprintf( pAO, "! and then drops again to 0%% at base position 800 or so.  This number\n");
    fprintf( pAO, "! specifies how high the number must be for Autofinish to consider an\n");
    fprintf( pAO, "! Autofinish read to cover a single subclone region.\n");
    fprintf( pAO, "! (OK)\n");
@@ -1295,7 +1295,7 @@
      ( ( pCP->bCheckIfTooManyWalks_ ) ? "true" : "false" ) );
 
    fprintf( pAO, "! this just checks if the number of walks, pcr ends, and unknown reads\n");
-   fprintf( pAO, "! exceeds 20% of the total number of reads.  If this is exceeded, then \n");
+   fprintf( pAO, "! exceeds 20%% of the total number of reads.  If this is exceeded, then \n");
    fprintf( pAO, "! a warning message is given.  Typically, such a warning indicates\n");
    fprintf( pAO, "! that you have incorrectly customized determineReadTypes.perl\n");
    fprintf( pAO, "! (OK)\n");
@@ -1446,7 +1446,7 @@
      ( ( pCP->bProcessMatePairsAtStartup_ ) ? "true" : "false" ) );
 
    fprintf( pAO, "! This is necessary to show the mate pair flags, but it does add\n");
-   fprintf( pAO, "! around 15% to startup time.\n");
+   fprintf( pAO, "! around 15%% to startup time.\n");
    fprintf( pAO, "! (OK)\n");
    fprintf( pAO, "consed.maximumNumberOfTracesShown: %d\n",
        pCP->nMaximumNumberOfTracesShown_ );
@@ -1796,7 +1796,7 @@
        (char*)pCP->soStoreTracePeakPositions_.data() );
 
    fprintf( pAO, "! never, always or whenChromatAvailable\n");
-   fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%,\n");
+   fprintf( pAO, "! changing this to \"always\" increases memory usage by close to 100%%,\n");
    fprintf( pAO, "! especially if the assembler is Newbler.  always means it will store\n");
    fprintf( pAO, "! the positions if they are present in the phd file/ball.\n");
    fprintf( pAO, "! \"whenChromatAvailable\" means it will store trace peak positions for\n");
--- a/readPrimerScreenSequences.cpp
+++ b/readPrimerScreenSequences.cpp
@@ -167,7 +167,7 @@
         ++nSequenceNumber ) {
       if ( pnLengthOfSequence[ nSequenceNumber ] !=
            strlen( pszSequence[ nSequenceNumber ] ) ) {
-         sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %d for sequence number %d",
+         sprintf( szErrorMessage, "inconsistency between pnLengthOfSequence %d and pszSequence %zu for sequence number %d",
                  pnLengthOfSequence[ nSequenceNumber ],
                  strlen( pszSequence[ nSequenceNumber ] ),
                         nSequenceNumber );
--- a/rwcstring.cpp
+++ b/rwcstring.cpp
@@ -235,7 +235,7 @@
 
    nMaxLength_ = nDefaultLengthForConversions;
 
-   nCurrentLength_ = sprintf( sz_, "%d", lNumberToConvert );
+   nCurrentLength_ = sprintf( sz_, "%ld", lNumberToConvert );
 
    if ( nCurrentLength_ > nMaxLength_ ) {
       // big trouble--might not even make it here--might segmentation fault
--- a/someOtherProgramSentACommandToConsed.cpp
+++ b/someOtherProgramSentACommandToConsed.cpp
@@ -89,7 +89,7 @@
 
    char szLine2[ nMaxLine ];
 
-   sprintf( szLine2, "# of chars = %d %s", strlen( szLine ), szLine );
+   sprintf( szLine2, "# of chars = %zu %s", strlen( szLine ), szLine );
 
    cout << szLine2 << endl;
 
--- a/tag.cpp
+++ b/tag.cpp
@@ -466,7 +466,7 @@
    fprintf( pPhdFile, "DATE: %s\n", soDate_.data() );
 
    if ( lID_ != nUndefinedTagID ) {
-      fprintf( pPhdFile, "ID: %d\n", lID_ );
+      fprintf( pPhdFile, "ID: %ld\n", lID_ );
    }
 
 
--- a/userDefinedTagField.cpp
+++ b/userDefinedTagField.cpp
@@ -64,7 +64,7 @@
 
 void userDefinedIntegerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) {
 
-   fprintf( pFile, "%s %d\n",
+   fprintf( pFile, "%s %ld\n",
                       pUserDefinedTagFieldType_->soFieldName_.data(),
                       l_ );
 }
@@ -119,7 +119,7 @@
 
 void userDefinedPointerTagField :: writeThyselfToAceFileOrPhdBall( FILE* pFile ) {
 
-   fprintf( pFile, "%s %d\n",
+   fprintf( pFile, "%s %ld\n",
             pUserDefinedTagFieldType_->soFieldName_.data(),
             lID_ );