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