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readability-implicit-bool-conversion
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@frederic-mahe
frederic-mahe committed Feb 10, 2025
1 parent 513f828 commit fdca407
Showing 1 changed file with 57 additions and 57 deletions.
114 changes: 57 additions & 57 deletions src/filter.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ inline auto fastq_get_qual(char q) -> int
"\n\nFatal error: FASTQ quality value (%d) below qmin (%"
PRId64 ")\n",
qual, opt_fastq_qmin);
if (fp_log)
if (fp_log != nullptr)
{
fprintf(stderr,
"\n\nFatal error: FASTQ quality value (%d) below qmin (%"
Expand All @@ -98,7 +98,7 @@ inline auto fastq_get_qual(char q) -> int
"By default, quality values range from 0 to 41.\n"
"To allow higher quality values, "
"please use the option --fastq_qmax %d\n", qual);
if (fp_log)
if (fp_log != nullptr)
{
fprintf(fp_log,
"\n\nFatal error: FASTQ quality value (%d) above qmax (%"
Expand Down Expand Up @@ -251,10 +251,10 @@ auto filter(bool fastq_only, char * filename) -> void
static constexpr auto dbl_max = std::numeric_limits<double>::max();
static constexpr auto long_min = std::numeric_limits<long>::min();

if ((not opt_fastqout) and (not opt_fastaout) and
(not opt_fastqout_discarded) and (not opt_fastaout_discarded) and
(not opt_fastqout_rev) and (not opt_fastaout_rev) and
(not opt_fastqout_discarded_rev) and (not opt_fastaout_discarded_rev))
if ((opt_fastqout == nullptr) and (opt_fastaout == nullptr) and
(opt_fastqout_discarded == nullptr) and (opt_fastaout_discarded == nullptr) and
(opt_fastqout_rev == nullptr) and (opt_fastaout_rev == nullptr) and
(opt_fastqout_discarded_rev == nullptr) and (opt_fastaout_discarded_rev == nullptr))
{
fatal("No output files specified");
}
Expand All @@ -264,7 +264,7 @@ auto filter(bool fastq_only, char * filename) -> void

h1 = fastx_open(filename);

if (not h1)
if (h1 == nullptr)
{
fatal("Unrecognized file type (not proper FASTA or FASTQ format)");
}
Expand All @@ -280,26 +280,26 @@ auto filter(bool fastq_only, char * filename) -> void
opt_fastq_eeout or
(opt_fastq_maxee < dbl_max) or
(opt_fastq_maxee_rate < dbl_max) or
opt_fastqout or
(opt_fastqout != nullptr) or
(opt_fastq_qmax < 41) or
(opt_fastq_qmin > 0) or
(opt_fastq_truncee < dbl_max) or
(opt_fastq_truncqual < long_min) or
opt_fastqout_discarded or
opt_fastqout_discarded_rev or
opt_fastqout_rev)
(opt_fastqout_discarded != nullptr) or
(opt_fastqout_discarded_rev != nullptr) or
(opt_fastqout_rev != nullptr))
{
fatal("The following options are not accepted with the fastx_filter command when the input is a FASTA file, because quality scores are not available: eeout, fastq_ascii, fastq_eeout, fastq_maxee, fastq_maxee_rate, fastq_out, fastq_qmax, fastq_qmin, fastq_truncee, fastq_truncqual, fastqout_discarded, fastqout_discarded_rev, fastqout_rev");
}
}

uint64_t const filesize = fastx_get_size(h1);

if (opt_reverse)
if (opt_reverse != nullptr)
{
h2 = fastx_open(opt_reverse);

if (not h2)
if (h2 == nullptr)
{
fatal("Unrecognized file type (not proper FASTA or FASTQ format) for reverse reads");
}
Expand All @@ -320,14 +320,14 @@ auto filter(bool fastq_only, char * filename) -> void
opt_fastq_eeout or
(opt_fastq_maxee < dbl_max) or
(opt_fastq_maxee_rate < dbl_max) or
opt_fastqout or
(opt_fastqout != nullptr) or
(opt_fastq_qmax < 41) or
(opt_fastq_qmin > 0) or
(opt_fastq_truncee < dbl_max) or
(opt_fastq_truncqual < long_min) or
opt_fastqout_discarded or
opt_fastqout_discarded_rev or
opt_fastqout_rev)
(opt_fastqout_discarded != nullptr) or
(opt_fastqout_discarded_rev != nullptr) or
(opt_fastqout_rev != nullptr))
{
fatal("The following options are not accepted with the fastx_filter command when the input is a FASTA file, because quality scores are not available: eeout, fastq_ascii, fastq_eeout, fastq_maxee, fastq_maxee_rate, fastq_out, fastq_qmax, fastq_qmin, fastq_truncee, fastq_truncqual, fastqout_discarded, fastqout_discarded_rev, fastqout_rev");
}
Expand All @@ -344,75 +344,75 @@ auto filter(bool fastq_only, char * filename) -> void
FILE * fp_fastaout_discarded_rev = nullptr;
FILE * fp_fastqout_discarded_rev = nullptr;

if (opt_fastaout)
if (opt_fastaout != nullptr)
{
fp_fastaout = fopen_output(opt_fastaout);
if (not fp_fastaout)
if (fp_fastaout == nullptr)
{
fatal("Unable to open FASTA output file for writing");
}
}

if (opt_fastqout)
if (opt_fastqout != nullptr)
{
fp_fastqout = fopen_output(opt_fastqout);
if (not fp_fastqout)
if (fp_fastqout == nullptr)
{
fatal("Unable to open FASTQ output file for writing");
}
}

if (opt_fastaout_discarded)
if (opt_fastaout_discarded != nullptr)
{
fp_fastaout_discarded = fopen_output(opt_fastaout_discarded);
if (not fp_fastaout_discarded)
if (fp_fastaout_discarded == nullptr)
{
fatal("Unable to open FASTA output file for writing");
}
}

if (opt_fastqout_discarded)
if (opt_fastqout_discarded != nullptr)
{
fp_fastqout_discarded = fopen_output(opt_fastqout_discarded);
if (not fp_fastqout_discarded)
if (fp_fastqout_discarded == nullptr)
{
fatal("Unable to open FASTQ output file for writing");
}
}

if (h2)
if (h2 != nullptr)
{
if (opt_fastaout_rev)
if (opt_fastaout_rev != nullptr)
{
fp_fastaout_rev = fopen_output(opt_fastaout_rev);
if (not fp_fastaout_rev)
if (fp_fastaout_rev == nullptr)
{
fatal("Unable to open FASTA output file for writing");
}
}

if (opt_fastqout_rev)
if (opt_fastqout_rev != nullptr)
{
fp_fastqout_rev = fopen_output(opt_fastqout_rev);
if (not fp_fastqout_rev)
if (fp_fastqout_rev == nullptr)
{
fatal("Unable to open FASTQ output file for writing");
}
}

if (opt_fastaout_discarded_rev)
if (opt_fastaout_discarded_rev != nullptr)
{
fp_fastaout_discarded_rev = fopen_output(opt_fastaout_discarded_rev);
if (not fp_fastaout_discarded_rev)
if (fp_fastaout_discarded_rev == nullptr)
{
fatal("Unable to open FASTA output file for writing");
}
}

if (opt_fastqout_discarded_rev)
if (opt_fastqout_discarded_rev != nullptr)
{
fp_fastqout_discarded_rev = fopen_output(opt_fastqout_discarded_rev);
if (not fp_fastqout_discarded_rev)
if (fp_fastqout_discarded_rev == nullptr)
{
fatal("Unable to open FASTQ output file for writing");
}
Expand All @@ -427,7 +427,7 @@ auto filter(bool fastq_only, char * filename) -> void

while (fastx_next(h1, false, chrmap_no_change))
{
if (h2 and not fastx_next(h2, false, chrmap_no_change))
if ((h2 != nullptr) and not fastx_next(h2, false, chrmap_no_change))
{
fatal("More forward reads than reverse reads");
}
Expand All @@ -437,7 +437,7 @@ auto filter(bool fastq_only, char * filename) -> void
struct analysis_res res2;

res1 = analyse(h1);
if (h2)
if (h2 != nullptr)
{
res2 = analyse(h2);
}
Expand All @@ -448,7 +448,7 @@ auto filter(bool fastq_only, char * filename) -> void

++discarded;

if (opt_fastaout_discarded)
if (opt_fastaout_discarded != nullptr)
{
fasta_print_general(fp_fastaout_discarded,
nullptr,
Expand All @@ -465,7 +465,7 @@ auto filter(bool fastq_only, char * filename) -> void
0.0);
}

if (opt_fastqout_discarded)
if (opt_fastqout_discarded != nullptr)
{
fastq_print_general(fp_fastqout_discarded,
fastx_get_sequence(h1) + res1.start,
Expand All @@ -478,9 +478,9 @@ auto filter(bool fastq_only, char * filename) -> void
res1.ee);
}

if (h2)
if (h2 != nullptr)
{
if (opt_fastaout_discarded_rev)
if (opt_fastaout_discarded_rev != nullptr)
{
fasta_print_general(fp_fastaout_discarded_rev,
nullptr,
Expand All @@ -497,7 +497,7 @@ auto filter(bool fastq_only, char * filename) -> void
0.0);
}

if (opt_fastqout_discarded_rev)
if (opt_fastqout_discarded_rev != nullptr)
{
fastq_print_general(fp_fastqout_discarded_rev,
fastx_get_sequence(h2) + res2.start,
Expand All @@ -522,7 +522,7 @@ auto filter(bool fastq_only, char * filename) -> void
++truncated;
}

if (opt_fastaout)
if (opt_fastaout != nullptr)
{
fasta_print_general(fp_fastaout,
nullptr,
Expand All @@ -539,7 +539,7 @@ auto filter(bool fastq_only, char * filename) -> void
0.0);
}

if (opt_fastqout)
if (opt_fastqout != nullptr)
{
fastq_print_general(fp_fastqout,
fastx_get_sequence(h1) + res1.start,
Expand All @@ -552,9 +552,9 @@ auto filter(bool fastq_only, char * filename) -> void
res1.ee);
}

if (h2)
if (h2 != nullptr)
{
if (opt_fastaout_rev)
if (opt_fastaout_rev != nullptr)
{
fasta_print_general(fp_fastaout_rev,
nullptr,
Expand All @@ -571,7 +571,7 @@ auto filter(bool fastq_only, char * filename) -> void
0.0);
}

if (opt_fastqout_rev)
if (opt_fastqout_rev != nullptr)
{
fastq_print_general(fp_fastqout_rev,
fastx_get_sequence(h2) + res2.start,
Expand All @@ -591,7 +591,7 @@ auto filter(bool fastq_only, char * filename) -> void

progress_done();

if (h2 and fastx_next(h2, false, chrmap_no_change))
if ((h2 != nullptr) and fastx_next(h2, false, chrmap_no_change))
{
fatal("More reverse reads than forward reads");
}
Expand All @@ -605,7 +605,7 @@ auto filter(bool fastq_only, char * filename) -> void
discarded);
}

if (opt_log)
if (opt_log != nullptr)
{
fprintf(fp_log,
"%" PRId64 " sequences kept (of which %" PRId64 " truncated), %" PRId64 " sequences discarded.\n",
Expand All @@ -614,47 +614,47 @@ auto filter(bool fastq_only, char * filename) -> void
discarded);
}

if (h2)
if (h2 != nullptr)
{
if (opt_fastaout_rev)
if (opt_fastaout_rev != nullptr)
{
fclose(fp_fastaout_rev);
}

if (opt_fastqout_rev)
if (opt_fastqout_rev != nullptr)
{
fclose(fp_fastqout_rev);
}

if (opt_fastaout_discarded_rev)
if (opt_fastaout_discarded_rev != nullptr)
{
fclose(fp_fastaout_discarded_rev);
}

if (opt_fastqout_discarded_rev)
if (opt_fastqout_discarded_rev != nullptr)
{
fclose(fp_fastqout_discarded_rev);
}

fastx_close(h2);
}

if (opt_fastaout)
if (opt_fastaout != nullptr)
{
fclose(fp_fastaout);
}

if (opt_fastqout)
if (opt_fastqout != nullptr)
{
fclose(fp_fastqout);
}

if (opt_fastaout_discarded)
if (opt_fastaout_discarded != nullptr)
{
fclose(fp_fastaout_discarded);
}

if (opt_fastqout_discarded)
if (opt_fastqout_discarded != nullptr)
{
fclose(fp_fastqout_discarded);
}
Expand Down

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