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-rw-r--r--sci-biology/consed/files/consed-29-fix-qa.patch294
1 files changed, 0 insertions, 294 deletions
diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch
deleted file mode 100644
index 90e180da0174..000000000000
--- a/sci-biology/consed/files/consed-29-fix-qa.patch
+++ /dev/null
@@ -1,294 +0,0 @@
-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_ );
-
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-06 09:45:56 +0000