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Avoid warning about missing space around literal #44

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Avoid warning about missing space around literal #44

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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ PROG = samblaster$(BUILDNUM)
CCFLAGS = -Wall -Winline -O0 -g -D BUILDNUM=$(BUILDNUM)
else
PROG = samblaster
CCFLAGS = -Wall -O3 -D BUILDNUM=$(BUILDNUM)
CCFLAGS = -Wall -Werror=literal-suffix -O3 -D BUILDNUM=$(BUILDNUM)
endif

CC = gcc
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26 changes: 13 additions & 13 deletions samblaster.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1115,7 +1115,7 @@ void markDupsDiscordants(splitLine_t * block, state_t * state)
#ifdef DEBUG
// This debug output allows the discovery of all members of a duplicate group including the read not marked as a duplicate.
// This could otherwise not be figured out from the output sam file.
fprintf(stderr, "%"PRIu64"\t%s\t%6d\t%s\t%"PRIu64"\t%s\n", idCount, second->fields[QNAME], second->flag, insert ? "First" : "Dup", sig, second->fields[RNAME]);
fprintf(stderr, "%" PRIu64 "\t%s\t%6d\t%s\t%" PRIu64 "\t%s\n", idCount, second->fields[QNAME], second->flag, insert ? "First" : "Dup", sig, second->fields[RNAME]);
#endif

// Check if the insertion actually happened.
Expand Down Expand Up @@ -1429,30 +1429,30 @@ void printRunStats(state_t * state)
if (!state->quiet)
{
if (state->discordantFile != NULL)
fprintf(stderr, "samblaster: Output %10"PRIu64" discordant read pairs to %s\n", discCount/2, state->discordantFileName);
fprintf(stderr, "samblaster: Output %10" PRIu64 " discordant read pairs to %s\n", discCount/2, state->discordantFileName);
if (state->splitterFile != NULL)
fprintf(stderr, "samblaster: Output %10"PRIu64" split reads to %s\n", splitCount, state->splitterFileName);
fprintf(stderr, "samblaster: Output %10" PRIu64 " split reads to %s\n", splitCount, state->splitterFileName);
if (state->unmappedClippedFile != NULL)
fprintf(stderr, "samblaster: Output %10"PRIu64" unmapped/clipped reads to %s\n", unmapClipCount, state->unmappedClippedFileName);
fprintf(stderr, "samblaster: Output %10" PRIu64 " unmapped/clipped reads to %s\n", unmapClipCount, state->unmappedClippedFileName);
}

// Now the stats that might indicate a problem that therefore deserve reporting even if quiet set.
if (readTooLongCount > 0)
{
fprintf(stderr, "samblaster: Found %10"PRIu64" of %10"PRIu64" (%5.3f) total read ids longer than the --maxReadLength(%d)\n."
fprintf(stderr, "samblaster: Found %10" PRIu64 " of %10" PRIu64 " (%5.3f) total read ids longer than the --maxReadLength(%d)\n."
"samblaster: The longest of which is %d bases long.\n",
readTooLongCount, idCount, ((double)100)*readTooLongCount/idCount, state->maxReadLength, readTooLongMax);
fprintf(stderr, "samblaster: Consider rerunning samblaster with a larger --maxReadLength.\n");
}
if (state->ignoreUnmated)
{
fprintf(stderr, "samblaster: Found %10"PRIu64" of %10"PRIu64" (%5.3f%%) total read ids are marked paired yet are unmated.\n",
fprintf(stderr, "samblaster: Found %10" PRIu64 " of %10" PRIu64 " (%5.3f%%) total read ids are marked paired yet are unmated.\n",
unmatedCount, idCount, ((double)100)*unmatedCount/idCount);
if (unmatedCount > 0) fprintf(stderr, "samblaster: Please double check that input file is read-id (QNAME) grouped.\n");
}
if (noPrimaryIdCount > 0)
{
fprintf(stderr, "samblaster: Found %10"PRIu64" of %10"PRIu64" (%5.3f%%) total read ids with no primary alignment.\n",
fprintf(stderr, "samblaster: Found %10" PRIu64 " of %10" PRIu64 " (%5.3f%%) total read ids with no primary alignment.\n",
noPrimaryIdCount, idCount, ((double)100)*noPrimaryIdCount/idCount);
if (unmatedCount > 0) fprintf(stderr, "samblaster: Please double check that input file is read-id (QNAME) grouped.\n");
}
Expand Down Expand Up @@ -1485,40 +1485,40 @@ void printRunStats(state_t * state)
// These first two can't produce any dups.
if (bothUnmappedIdCount > 0)
{
fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n",
fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n",
typeLength, typeLength, "Both Unmapped ",
bothUnmappedIdCount, ((double)100)*bothUnmappedIdCount/idCount, (UINT64)0, (double)0, (double)0, (double)0);
}
if (unmappedOrphanIdCount > 0)
{
fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n",
fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n",
typeLength, typeLength, "Unmapped Orphan/Singleton ",
unmappedOrphanIdCount, ((double)100)*unmappedOrphanIdCount/idCount, (UINT64)0, (double)0, (double)0, (double)0);
}
// All orphanDups are, of course, from mapped orphans.
if (mappedOrphanIdCount > 0)
{
fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n",
fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n",
typeLength, typeLength, orphanString,
mappedOrphanIdCount, ((double)100)*mappedOrphanIdCount/idCount, orphanDupCount,
((double)100)*orphanDupCount/mappedOrphanIdCount, ((double)100)*orphanDupCount/dupCount, ((double)100)*orphanDupCount/idCount);
}
if (bothMappedIdCount > 0)
{
fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n",
fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n",
typeLength, typeLength, "Both Mapped ",
bothMappedIdCount, ((double)100)*bothMappedIdCount/idCount, bothMappedDupCount, ((double)100)*bothMappedDupCount/bothMappedIdCount,
((double)100)*bothMappedDupCount/dupCount, ((double)100)*bothMappedDupCount/idCount);
}
fprintf(stderr, "samblaster: %*.*s %10"PRIu64" %7.3f %10"PRIu64" %7.3f %7.3f %7.3f\n",
fprintf(stderr, "samblaster: %*.*s %10" PRIu64 " %7.3f %10" PRIu64 " %7.3f %7.3f %7.3f\n",
typeLength, typeLength, "Total ",
idCount, ((double)100)*idCount/idCount, dupCount,
((double)100)*dupCount/idCount, (double)100, ((double)100)*dupCount/idCount);
fprintf(stderr, "samblaster:\n");
}
// Output the main conclusion even if we output the table.
// It includes the fact of whether or not the dups were marked or removed, and the timing info.
fprintf(stderr, "samblaster: %s %10"PRIu64" of %10"PRIu64" (%5.3f%%) total read ids as duplicates",
fprintf(stderr, "samblaster: %s %10" PRIu64 " of %10" PRIu64 " (%5.3f%%) total read ids as duplicates",
(state->removeDups ? "Removed" : "Marked "), dupCount, idCount, ((double)100)*dupCount/idCount);
if ((TIMING == 0) || state->quiet)
{
Expand Down