From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-biology/consed/files/consed-29-fix-qa.patch | 275 ++++++++++++++++++++++++ 1 file changed, 275 insertions(+) create mode 100644 sci-biology/consed/files/consed-29-fix-qa.patch (limited to 'sci-biology/consed/files/consed-29-fix-qa.patch') diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch new file mode 100644 index 000000000000..5bdf0264d25b --- /dev/null +++ b/sci-biology/consed/files/consed-29-fix-qa.patch @@ -0,0 +1,275 @@ +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/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_ ); + -- cgit v1.2.3