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Rename local variables for consistency.
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@brianwalenz
brianwalenz committed Sep 27, 2020
1 parent a8b31c7 commit ad130cc
Showing 1 changed file with 43 additions and 43 deletions.
86 changes: 43 additions & 43 deletions src/stores/sqStoreDumpMetaData.C
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Original file line number Diff line number Diff line change
Expand Up @@ -97,26 +97,26 @@ dumpReads_printHeader(sqRead_which w) {


bool
dumpReads_setClearString(sqStore *seqs, uint32 rid, char *len, char *bgn, char *end, sqRead_which w) {
dumpReads_setClearString(sqStore *seq, uint32 rid, char *len, char *bgn, char *end, sqRead_which w) {

// Set the length of the read.

if (seqs->sqStore_isValidRead(rid, w) == false)
if (seq->sqStore_isValidRead(rid, w) == false)
memcpy(len, " -", sizeof(char) * 11);

else if (seqs->sqStore_isIgnoredRead(rid, w) == true)
else if (seq->sqStore_isIgnoredRead(rid, w) == true)
memcpy(len, " ignored", sizeof(char) * 11);

else
snprintf(len, 12, " %10" F_U32P, seqs->sqStore_getReadLength(rid, w));
snprintf(len, 12, " %10" F_U32P, seq->sqStore_getReadLength(rid, w));

assert((w & sqRead_trimmed) == sqRead_unset); // Otherwise, length above is trimmed length!

// Set the clear range.

if (seqs->sqStore_isTrimmedRead(rid, w) == true) {
snprintf(bgn, 12, " %10" F_U32P, seqs->sqStore_getClearBgn(rid, w | sqRead_trimmed));
snprintf(end, 12, " %10" F_U32P, seqs->sqStore_getClearEnd(rid, w | sqRead_trimmed));
if (seq->sqStore_isTrimmedRead(rid, w) == true) {
snprintf(bgn, 12, " %10" F_U32P, seq->sqStore_getClearBgn(rid, w | sqRead_trimmed));
snprintf(end, 12, " %10" F_U32P, seq->sqStore_getClearEnd(rid, w | sqRead_trimmed));
} else {
memcpy(bgn, " -", sizeof(char) * 11);
memcpy(end, " -", sizeof(char) * 11);
Expand All @@ -126,17 +126,17 @@ dumpReads_setClearString(sqStore *seqs, uint32 rid, char *len, char *bgn, char *
bgn[11] = 0;
end[11] = 0;

return(seqs->sqStore_isValidRead(rid, w));
return(seq->sqStore_isValidRead(rid, w));
}



void
dumpReads_setFlagsString(sqStore *seqs, uint32 rid, char *flags) {
bool rv = seqs->sqStore_isValidRead (rid, sqRead_raw);
bool rt = seqs->sqStore_isTrimmedRead(rid, sqRead_raw);
bool cv = seqs->sqStore_isValidRead (rid, sqRead_corrected);
bool ct = seqs->sqStore_isTrimmedRead(rid, sqRead_corrected);
dumpReads_setFlagsString(sqStore *seq, uint32 rid, char *flags) {
bool rv = seq->sqStore_isValidRead (rid, sqRead_raw);
bool rt = seq->sqStore_isTrimmedRead(rid, sqRead_raw);
bool cv = seq->sqStore_isValidRead (rid, sqRead_corrected);
bool ct = seq->sqStore_isTrimmedRead(rid, sqRead_corrected);

flags[0] = 'r'; // Default to non-valid raw and corrected reads.
flags[1] = '-';
Expand All @@ -150,21 +150,21 @@ dumpReads_setFlagsString(sqStore *seqs, uint32 rid, char *flags) {

if (rv) {
flags[0] = 'R';
flags[1] = (seqs->sqStore_isIgnoredRead(rid, sqRead_raw)) ? 'I' : 'R';
flags[1] = (seq->sqStore_isIgnoredRead(rid, sqRead_raw)) ? 'I' : 'R';

if (rt) {
flags[2] = 'T';
flags[3] = (seqs->sqStore_isIgnoredRead(rid, sqRead_raw | sqRead_trimmed)) ? 'I' : 'T';
flags[3] = (seq->sqStore_isIgnoredRead(rid, sqRead_raw | sqRead_trimmed)) ? 'I' : 'T';
}
}

if (cv) {
flags[4] = 'C';
flags[5] = (seqs->sqStore_isIgnoredRead(rid, sqRead_corrected)) ? 'I' : 'C';
flags[5] = (seq->sqStore_isIgnoredRead(rid, sqRead_corrected)) ? 'I' : 'C';

if (ct) {
flags[6] = 'T';
flags[7] = (seqs->sqStore_isIgnoredRead(rid, sqRead_corrected | sqRead_trimmed)) ? 'I' : 'T';
flags[7] = (seq->sqStore_isIgnoredRead(rid, sqRead_corrected | sqRead_trimmed)) ? 'I' : 'T';
}
}

Expand All @@ -174,8 +174,8 @@ dumpReads_setFlagsString(sqStore *seqs, uint32 rid, char *flags) {


void
dumpReads(sqStore *seqs, uint32 bgnID, uint32 endID, sqRead_which w, bool showAll) {
uint32 lastRead = seqs->sqStore_lastReadID();
dumpReads(sqStore *seq, uint32 bgnID, uint32 endID, sqRead_which w, bool showAll) {
uint32 lastRead = seq->sqStore_lastReadID();

assert(bgnID >= 1);
assert(bgnID <= lastRead);
Expand All @@ -196,37 +196,37 @@ dumpReads(sqStore *seqs, uint32 bgnID, uint32 endID, sqRead_which w, bool showAl
for (uint32 rid=bgnID; rid<=endID; rid++) {
bool active = showAll;

dumpReads_setClearString(seqs, rid, s1len, s1bgn, s1end, sqRead_raw);
dumpReads_setClearString(seqs, rid, s2len, s2bgn, s2end, sqRead_raw | sqRead_compressed);
dumpReads_setClearString(seqs, rid, s3len, s3bgn, s3end, sqRead_corrected);
dumpReads_setClearString(seqs, rid, s4len, s4bgn, s4end, sqRead_corrected | sqRead_compressed);
dumpReads_setFlagsString(seqs, rid, flags);
dumpReads_setClearString(seq, rid, s1len, s1bgn, s1end, sqRead_raw);
dumpReads_setClearString(seq, rid, s2len, s2bgn, s2end, sqRead_raw | sqRead_compressed);
dumpReads_setClearString(seq, rid, s3len, s3bgn, s3end, sqRead_corrected);
dumpReads_setClearString(seq, rid, s4len, s4bgn, s4end, sqRead_corrected | sqRead_compressed);
dumpReads_setFlagsString(seq, rid, flags);

l1[0] = 0;

if ((w == sqRead_unset) || (((w & sqRead_raw) != 0) && ((w & sqRead_compressed) == 0))) {
active |= seqs->sqStore_isValidRead(rid, sqRead_raw);
active |= seq->sqStore_isValidRead(rid, sqRead_raw);
strcat(l1, s1len);
strcat(l1, s1bgn);
strcat(l1, s1end);
}

if ((w == sqRead_unset) || (((w & sqRead_raw) != 0) && ((w & sqRead_compressed) != 0))) {
active |= seqs->sqStore_isValidRead(rid, sqRead_raw);
active |= seq->sqStore_isValidRead(rid, sqRead_raw);
strcat(l1, s2len);
strcat(l1, s2bgn);
strcat(l1, s2end);
}

if ((w == sqRead_unset) || (((w & sqRead_corrected) != 0) && ((w & sqRead_compressed) == 0))) {
active |= seqs->sqStore_isValidRead(rid, sqRead_corrected);
active |= seq->sqStore_isValidRead(rid, sqRead_corrected);
strcat(l1, s3len);
strcat(l1, s3bgn);
strcat(l1, s3end);
}

if ((w == sqRead_unset) || (((w & sqRead_corrected) != 0) && ((w & sqRead_compressed) != 0))) {
active |= seqs->sqStore_isValidRead(rid, sqRead_corrected);
active |= seq->sqStore_isValidRead(rid, sqRead_corrected);
strcat(l1, s4len);
strcat(l1, s4bgn);
strcat(l1, s4end);
Expand All @@ -235,11 +235,11 @@ dumpReads(sqStore *seqs, uint32 bgnID, uint32 endID, sqRead_which w, bool showAl
if (active)
fprintf(stdout, "%10" F_U32P " %10" F_U32P "%s %s %4lu %12lu\n",
rid,
seqs->sqStore_getLibraryIDForRead(rid),
seq->sqStore_getLibraryIDForRead(rid),
l1,
flags,
seqs->sqStore_getReadSegm(rid),
seqs->sqStore_getReadByte(rid));
seq->sqStore_getReadSegm(rid),
seq->sqStore_getReadByte(rid));
}
}

Expand All @@ -251,23 +251,23 @@ doSummarize_lengthHistogram(vector<uint64> lengths,


void
dumpHistogram(sqStore *seqs, uint32 bgnID, uint32 endID, bool dumpLengths) {
dumpHistogram(sqStore *seq, uint32 bgnID, uint32 endID, bool dumpLengths) {
vector<uint64> lengths;
uint64 nBases = 0;

// Build a vector of sequence lengths, pass that to 'sequence' to
// generate a pretty picture.

for (uint32 rid=bgnID; rid<=endID; rid++) {
uint32 len = seqs->sqStore_getReadLength(rid);
uint32 len = seq->sqStore_getReadLength(rid);

if (seqs->sqStore_isValidRead(rid) == false) // Skip invalid reads.
if (seq->sqStore_isValidRead(rid) == false) // Skip invalid reads.
continue;

if (seqs->sqStore_isIgnoredRead(rid) == true) // Skip ignored reads.
if (seq->sqStore_isIgnoredRead(rid) == true) // Skip ignored reads.
continue;

if ((seqs->sqStore_isTrimmedRead(rid) == false) && // Skip untrimmed reads,
if ((seq->sqStore_isTrimmedRead(rid) == false) && // Skip untrimmed reads,
(sqRead_defaultVersion & sqRead_trimmed)) // if we want trimmed reads.
continue;

Expand Down Expand Up @@ -302,7 +302,7 @@ dumpHistogram(sqStore *seqs, uint32 bgnID, uint32 endID, bool dumpLengths) {


sqStoreInfo
getStats(sqStore *seqs, uint32 bgnID, uint32 endID) {
getStats(sqStore *seq, uint32 bgnID, uint32 endID) {
sqStoreInfo info;
sqRead_which w1 = sqRead_raw;
sqRead_which w2 = sqRead_raw | sqRead_compressed;
Expand All @@ -312,10 +312,10 @@ getStats(sqStore *seqs, uint32 bgnID, uint32 endID) {
for (uint32 rid=bgnID; rid<=endID; rid++) {
bool exists = false;

exists |= info.examineRead(rid, seqs->sqStore_getReadSeq(rid, w1), w1);
exists |= info.examineRead(rid, seqs->sqStore_getReadSeq(rid, w2), w2);
exists |= info.examineRead(rid, seqs->sqStore_getReadSeq(rid, w3), w3);
exists |= info.examineRead(rid, seqs->sqStore_getReadSeq(rid, w4), w4);
exists |= info.examineRead(rid, seq->sqStore_getReadSeq(rid, w1), w1);
exists |= info.examineRead(rid, seq->sqStore_getReadSeq(rid, w2), w2);
exists |= info.examineRead(rid, seq->sqStore_getReadSeq(rid, w3), w3);
exists |= info.examineRead(rid, seq->sqStore_getReadSeq(rid, w4), w4);

if (exists)
info.sqInfo_addRead();
Expand All @@ -327,8 +327,8 @@ getStats(sqStore *seqs, uint32 bgnID, uint32 endID) {


void
dumpStats(sqStore *seqs, uint32 bgnID, uint32 endID) {
getStats(seqs, bgnID, endID).writeInfoAsText(stdout);
dumpStats(sqStore *seq, uint32 bgnID, uint32 endID) {
getStats(seq, bgnID, endID).writeInfoAsText(stdout);
}


Expand Down

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