f8b37f0a0b7ac9bbd5529692fa61b921a6a2b67f hiram Fri Jul 7 23:57:27 2017 -0700 check in before removing all the garbage, appears to be working with arrays much faster refs #18969 diff --git src/utils/crisprKmers/crisprKmers.c src/utils/crisprKmers/crisprKmers.c index a1e0304..6149968 100644 --- src/utils/crisprKmers/crisprKmers.c +++ src/utils/crisprKmers/crisprKmers.c @@ -1,790 +1,1116 @@ /* crisprKmers - find and annotate crispr sequences. */ #include #include "common.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "dnautil.h" #include "dnaseq.h" #include "dnaLoad.h" #include "portable.h" #include "basicBed.h" #include "sqlNum.h" #include "binRange.h" #include "obscure.h" +#include "memalloc.h" void usage() /* Explain usage and exit. */ { errAbort( "crisprKmers - annotate crispr sequences\n" "usage:\n" " crisprKmers \n" "options:\n" " where is a .2bit file or .fa fasta sequence\n" " -verbose=N - control processing steps with level of verbose:\n" " default N=1 - only find crisprs, set up listings\n" " N=2 - empty process crispr list into new list\n" " N=3 - only count identicals during processing\n" " N=4 - attempt measure all off targets and\n" " print out all crisprs as bed format\n" " -bed= - output kmers to given bed9+ file\n" " -ranges= - use specified bed3 file to limit which crisprs are\n" " - measured, only those with any overlap to these bed items.\n" " -dumpKmers= - after scan of sequence, output kmers to file\n" " - process will exit after this, use -loadKmers to continue\n" " -loadKmers= - load kmers from previous scan of sequence from -dumpKmers\n" " NOTE: It is faster to simply scan the sequence to get the system ready\n" " to go. Reading in the kmer file takes longer than scanning." ); } static char *bedFileOut = NULL; /* set with -bed= argument */ static char *ranges = NULL; /* set with -ranges= argument */ static struct hash *rangesHash = NULL; /* ranges into hash + binkeeper */ static char *dumpKmers = NULL; /* file name to write out kmers from scan */ static char *loadKmers = NULL; /* file name to read in kmers from previous scan */ /* Command line validation table. */ static struct optionSpec options[] = { {"bed", OPTION_STRING}, {"ranges", OPTION_STRING}, {"dumpKmers", OPTION_STRING}, {"loadKmers", OPTION_STRING}, {NULL, 0}, }; struct crispr /* one chromosome set of crisprs */ { struct crispr *next; /* Next in list. */ long long sequence; /* sequence value in 2bit format */ long long start; /* chromosome start 0-relative */ char strand; /* strand: + or - */ int offBy0; /* counting number of off targets, 0 mismatch */ int offBy1; /* counting number of off targets, 1 mismatch */ int offBy2; /* counting number of off targets, 2 mismatch */ int offBy3; /* counting number of off targets, 3 mismatch */ int offBy4; /* counting number of off targets, 4 mismatch */ }; struct crisprList /* all chromosome sets of crisprs */ { struct crisprList *next; /* Next in list. */ char *chrom; /* chrom name */ int size; /* chrom size */ struct crispr *chromCrisprs; /* all the crisprs on this chrom */ long long crisprCount; /* number of crisprs on this chrom */ + long long *sequence; /* array of the sequences */ + long long *start; /* array of the starts */ + char *strand; /* array of the strand characters */ + int **offBy; /* offBy[5][n] */ }; #define A_BASE 0 #define C_BASE 1 #define G_BASE 2 #define T_BASE 3 #define U_BASE 3 static int orderedNtVal[256]; /* values in alpha order: ACGT 00 01 10 11 */ /* for easier sorting and complementing */ static char bases[4]; /* for binary to ascii conversion */ #define fortySixBits 0x3fffffffffff #define fortyEixhtBits 0xffffffffffff #define high32bits 0xffffffff00000000 #define low32bits 0x00000000ffffffff #define high16bits 0xffff0000ffff0000 #define low16bits 0x0000ffff0000ffff #define high8bits 0xff00ff00ff00ff00 #define low8bits 0x00ff00ff00ff00ff #define high4bits 0xf0f0f0f0f0f0f0f0 #define low4bits 0x0f0f0f0f0f0f0f0f #define high2bits 0xcccccccccccccccc #define low2bits 0x3333333333333333 static void initOrderedNtVal() /* initialization of base value lookup arrays */ { int i; for (i=0; i 0) perSecond = 1000.0 * count / ms; verbose(1, "# %s: %lld %s @ %ld ms -> %.2f %s\n", prefix, count, message, ms, perSecond, units); } static struct hash *readRanges(char *bedFile) /* Read bed and return it as a hash keyed by chromName * with binKeeper values. (from: src/hg/bedIntersect/bedIntersec.c) */ { struct hash *hash = newHash(0); /* key is chromName, value is binkeeper data */ struct lineFile *lf = lineFileOpen(bedFile, TRUE); char *row[3]; while (lineFileNextRow(lf, row, 3)) { struct binKeeper *bk; struct bed3 *item; struct hashEl *hel = hashLookup(hash, row[0]); if (hel == NULL) { bk = binKeeperNew(0, 1024*1024*1024); hel = hashAdd(hash, row[0], bk); } bk = hel->val; AllocVar (item); item->chrom = hel->name; item->chromStart = lineFileNeedNum(lf, row, 1); item->chromEnd = lineFileNeedNum(lf, row, 2); binKeeperAdd(bk, item->chromStart, item->chromEnd, item); } lineFileClose(&lf); return hash; } // static struct hash *readRanges(char *bedFile) #ifdef NOT // Do not need this, slReverse does this job, perhaps a bit more efficiently static int slCmpStart(const void *va, const void *vb) /* Compare slPairs on start value */ { const struct crispr *a = *((struct crispr **)va); const struct crispr *b = *((struct crispr **)vb); long long aVal = a->start; long long bVal = b->start; if (aVal < bVal) return -1; else if (aVal > bVal) return 1; else return 0; } #endif +static char *kmerPAMStringArray(long long val) +/* return the ASCII string for last three bases in then binary sequence value */ +{ +static char pamString[32]; +long long twoBitMask = 0x30; +int shiftCount = 4; +int baseCount = 0; + +while (twoBitMask) + { + int base = (val & twoBitMask) >> shiftCount; + pamString[baseCount++] = bases[base]; + twoBitMask >>= 2; + shiftCount -= 2; + } +pamString[baseCount] = 0; +return pamString; +} // static char *kmerValToStringArray(struct crispr *c, int trim) + +#ifdef NOT static char *kmerPAMString(struct crispr *c) /* return the ASCII string for last three bases in then binary sequence value */ { long long val = c->sequence; static char pamString[32]; long long twoBitMask = 0x30; int shiftCount = 4; int baseCount = 0; while (twoBitMask) { int base = (val & twoBitMask) >> shiftCount; pamString[baseCount++] = bases[base]; twoBitMask >>= 2; shiftCount -= 2; } pamString[baseCount] = 0; return pamString; -} // static char *kmerValToString(struct crispr *c, int trim) +} // static char *kmerPAMString(struct crispr *c) +#endif +static char *kmerValToStringArray(long long val, int trim) +/* return ASCII string for binary sequence value */ +{ +static char kmerString[32]; +long long twoBitMask = 0x300000000000; +int shiftCount = 44; +int baseCount = 0; + +while (twoBitMask && (shiftCount >= (2*trim))) + { + int base = (val & twoBitMask) >> shiftCount; + kmerString[baseCount++] = bases[base]; + twoBitMask >>= 2; + shiftCount -= 2; + } +kmerString[baseCount] = 0; +return kmerString; +} // static char *kmerValToStringArray(long long val, int trim) + +#ifdef NOT static char *kmerValToString(struct crispr *c, int trim) /* print out ASCII string for binary sequence value */ { long long val = c->sequence; static char kmerString[32]; long long twoBitMask = 0x300000000000; int shiftCount = 44; int baseCount = 0; while (twoBitMask && (shiftCount >= (2*trim))) { int base = (val & twoBitMask) >> shiftCount; kmerString[baseCount++] = bases[base]; twoBitMask >>= 2; shiftCount -= 2; } kmerString[baseCount] = 0; return kmerString; } // static char *kmerValToString(struct crispr *c, int trim) - +#endif static long long revComp(long long val) /* reverse complement the 2-bit numerical value kmer */ { /* complement bases and add 18 0 bits * because this divide and conquer works on 64 bits, not 46, * hence the addition of the 18 zero bits which fall out * The 'val ^ fortySixBits' does the complement, the shifting and * masking does the reversing. */ register long long v = (val ^ fortySixBits) << 18; v = ((v & high32bits) >> 32) | ((v & low32bits) << 32); v = ((v & high16bits) >> 16) | ((v & low16bits) << 16); v = ((v & high8bits) >> 8) | ((v & low8bits) << 8); v = ((v & high4bits) >> 4) | ((v & low4bits) << 4); v = ((v & high2bits) >> 2) | ((v & low2bits) << 2); return v; } // static long long revComp(long long val) +static void copyToArray(struct crisprList *list) +/* copy the crispr list data into arrays */ +{ +verbose(1, "# copyToArray(%p)\n", (void *)list); +struct crisprList *cl = NULL; +for (cl = list; cl; cl = cl->next) + { + verbose(1, "# copy %p %lld crisprs for chrom %s\n", (void *)cl, cl->crisprCount, cl->chrom); + size_t memSize = cl->crisprCount * sizeof(long long); + cl->sequence = (long long *)needLargeMem(memSize); + cl->start = (long long *)needLargeMem(memSize); + memSize = cl->crisprCount * sizeof(char); + cl->strand = (char *)needLargeMem(memSize); + memSize = 5 * sizeof(int *); + cl->offBy = (int **)needLargeMem(memSize); + memSize = cl->crisprCount * sizeof(int); + int r = 0; + for (r = 0; r < 5; ++r) + cl->offBy[r] = (int *)needLargeZeroedMem(memSize); + + long long i = 0; + struct crispr *c = NULL; + for (c = cl->chromCrisprs; c; c = c->next) + { + #ifdef NOT + if (2 > i) { + verbose(1, "# list: %#llx\n", (unsigned long long)cl); + verbose(1, "# list->sequence: %#llx\n", (unsigned long long)cl->sequence); + verbose(1, "# list->sequence[%lld]: %#llx\n", i, (unsigned long long)&cl->sequence[i]); + verbose(1, "# list->strand: %#llx\n", (unsigned long long)cl->strand); + verbose(1, "# list->strand[%lld]: %#llx\n", i, (unsigned long long)&cl->strand[i]); + } + #endif + cl->sequence[i] = c->sequence; + cl->start[i] = c->start; + cl->strand[i++] = c->strand; + } + } +} // static void copyToArray(struct crisprList *list) */ + static struct crisprList *generateKmers(struct dnaSeq *seq) { struct crispr *crisprSet = NULL; struct crisprList *returnList = NULL; AllocVar(returnList); returnList->chrom = cloneString(seq->name); returnList->size = seq->size; int i; DNA *dna; long long chromPosition = 0; long long startGap = 0; long long gapCount = 0; int kmerLength = 0; long long kmerVal = 0; long long endsGG = (G_BASE << 2) | G_BASE; long long beginsCC = (long long)((C_BASE << 2) | C_BASE) << 42; long long reverseMask = (long long)0xf << 42; verbose(4, "# endsGG: %032llx\n", endsGG); verbose(4, "# beginsCC: %032llx\n", beginsCC); verbose(4, "# 46 bits: %032llx\n", (long long) fortySixBits); dna=seq->dna; for (i=0; i < seq->size; ++i) { int val = orderedNtVal[(int)dna[i]]; if (val >= 0) { kmerVal = fortySixBits & ((kmerVal << 2) | val); ++kmerLength; if (kmerLength > 22) { if (endsGG == (kmerVal & 0xf)) /* check positive strand */ { struct crispr *oneCrispr = NULL; AllocVar(oneCrispr); oneCrispr->start = chromPosition - 22; oneCrispr->strand = '+'; oneCrispr->sequence = kmerVal; slAddHead(&crisprSet, oneCrispr); } if (beginsCC == (kmerVal & reverseMask)) /* check neg strand */ { struct crispr *oneCrispr = NULL; AllocVar(oneCrispr); oneCrispr->start = chromPosition - 22; oneCrispr->strand = '-'; oneCrispr->sequence = revComp(kmerVal); slAddHead(&crisprSet, oneCrispr); } } } // if (val >= 0) else { ++gapCount; startGap = chromPosition; /* skip all N's == any value not = 0,1,2,3 */ while ( ((i+1) < seq->size) && (orderedNtVal[(int)dna[i+1]] < 0)) { ++chromPosition; ++i; } if (startGap != chromPosition) verbose(4, "#GAP %s\t%lld\t%lld\t%lld\t%lld\t%s\n", seq->name, startGap, chromPosition, gapCount, chromPosition-startGap, "+"); else verbose(4, "#GAP %s\t%lld\t%lld\t%lld\t%lld\t%s\n", seq->name, startGap, chromPosition+1, gapCount, 1+chromPosition-startGap, "+"); kmerLength = 0; /* reset, start over */ kmerVal = 0; } // else if (val >= 0) ++chromPosition; } // for (i=0; i < seq->size; ++i) // slReverse(&crisprSet); // save time, order not important at this time returnList->chromCrisprs = crisprSet; returnList->crisprCount = slCount(crisprSet); return returnList; } // static struct crisprList *generateKmers(struct dnaSeq *seq) +static void showCountsArray(struct crisprList *all) +/* everything has been scanned and counted, print out all the data from arrays*/ +{ +FILE *bedFH = NULL; +if (bedFileOut) + bedFH = mustOpen(bedFileOut, "w"); + +verbose(1, "#\tprint out all data\n"); +struct crisprList *list; +long long totalOut = 0; +verbose(1, "# %d number of chromosomes to display\n", slCount(all)); +for (list = all; list; list = list->next) + { + verbose(1, "# crisprs count %lld on chrom %s\n", list->crisprCount, list->chrom); + long long c = 0; + for (c = 0; c < list->crisprCount; ++c) + { + int negativeOffset = 0; + if (list->strand[c] == '-') + negativeOffset = 3; + long long txStart = list->start[c] + negativeOffset; + long long txEnd = txStart + 20 + negativeOffset; + int totalOffs = list->offBy[0][c] + list->offBy[1][c] + + list->offBy[2][c] + list->offBy[3][c] + list->offBy[4][c]; + + if (0 == totalOffs) +verbose(1, "# PERFECT score %s:%lld %c\t%s\n", list->chrom, list->start[c], list->strand[c], kmerValToStringArray(list->sequence[c], 3)); + + if (bedFH) + fprintf(bedFH, "%s\t%lld\t%lld\t%s\t%d\t%c\t%lld\t%lld\t%s\t%d\t%d\t%d\t%d\n", list->chrom, list->start[c], list->start[c]+23, kmerValToStringArray(list->sequence[c], 3), list->offBy[0][c], list->strand[c], txStart, txEnd, kmerPAMStringArray(list->sequence[c]), list->offBy[1][c], list->offBy[2][c], list->offBy[3][c], list->offBy[4][c]); + + if (list->offBy[0][c]) + verbose(3, "# array identical: %d %s:%lld %c\t%s\n", list->offBy[0][c], list->chrom, list->start[c], list->strand[c], kmerValToStringArray(list->sequence[c], 3)); + ++totalOut; + } + } +verbose(1, "# total Array crisprs displayed: %lld\n", totalOut); +if (bedFH) + carefulClose(&bedFH); +} // static void showCountsArray(struct crisprList *all) + +#ifdef NOT static void showCounts(struct crisprList *all) /* everything has been scanned and counted, print out all the data */ { FILE *bedFH = NULL; if (bedFileOut) bedFH = mustOpen(bedFileOut, "w"); verbose(1, "#\tprint out all data\n"); struct crisprList *list; long long totalChecked = 0; verbose(1, "# %d number of chromosomes to display\n", slCount(all)); for (list = all; list; list = list->next) { struct crispr *c = NULL; struct crispr *next = NULL; verbose(1, "# crisprs count %lld on chrom %s\n", list->crisprCount, list->chrom); for (c = list->chromCrisprs; c; c = next) { int negativeOffset = 0; if (c->strand == '-') negativeOffset = 3; long long txStart = c->start + negativeOffset; long long txEnd = c->start+20 + negativeOffset; if (bedFH) fprintf(bedFH, "%s\t%lld\t%lld\t%s\t%d\t%c\t%lld\t%lld\t%s\t%d\t%d\t%d\t%d\n", list->chrom, c->start, c->start+23, kmerValToString(c, 3), c->offBy0, c->strand, txStart, txEnd, kmerPAMString(c), c->offBy1, c->offBy2, c->offBy3, c->offBy4); if (c->offBy0) verbose(3, "# identical: %d %s:%lld %c\t%s\n", c->offBy0, list->chrom, c->start, c->strand, kmerValToString(c, 3)); next = c->next; ++totalChecked; } } verbose(1, "# total crisprs displayed: %lld\n", totalChecked); if (bedFH) carefulClose(&bedFH); } // static void showCounts(struct crisprList *all) +#endif +#ifdef NOT static long long countOffTargets(char *chrom, struct crispr *c, struct crisprList *all) /* given one crispr c, scan against all others to find off targets */ { struct crisprList *listPtr; long long totalCompares = 0; for (listPtr = all; listPtr; listPtr = listPtr->next) { struct crispr *crisprPtr = NULL; struct crispr *next = NULL; for (crisprPtr = listPtr->chromCrisprs; crisprPtr; crisprPtr = next) { /* the XOR will determine differences in two sequences * the shift right 6 removes the PAM sequence */ long long misMatch = (c->sequence ^ crisprPtr->sequence) >> 6; if (! misMatch) /* no misMatch, identical crisprs */ { c->offBy0 += 1; crisprPtr->offBy0 += 1; } else { if (verboseLevel() > 2) { /* possible misMatch bit values: 01 10 11 * turn those three values into just: 01 */ misMatch = (misMatch | (misMatch > 1)) & 0x5555555555; int bitsOn = _mm_popcnt_u64(misMatch); switch(bitsOn) { case 1: c->offBy1 += 1; crisprPtr->offBy1 += 1; break; case 2: c->offBy2 += 1; crisprPtr->offBy2 += 1; break; case 3: c->offBy3 += 1; crisprPtr->offBy3 += 1; break; case 4: c->offBy4 += 1; crisprPtr->offBy4 += 1; break; default: break; } } } ++totalCompares; next = crisprPtr->next; } } return totalCompares; } // static void countOffTargets( . . . ) +#endif static struct crisprList *scanSequence(char *inFile) /* scan the given file, return list of crisprs */ { verbose(1, "#\tscanning sequence file: %s\n", inFile); dnaUtilOpen(); struct dnaLoad *dl = dnaLoadOpen(inFile); struct dnaSeq *seq; struct crisprList *listReturn = NULL; long elapsedMs = 0; long scanStart = clock1000(); long long totalCrisprs = 0; /* scanning all sequences, setting up crisprs on the listReturn */ while ((seq = dnaLoadNext(dl)) != NULL) { if (startsWithNoCase("chrUn", seq->name) || rStringIn("hap", seq->name) || rStringIn("_alt", seq->name) ) { verbose(1, "# skip chrom: %s\n", seq->name); continue; } long startTime = clock1000(); struct crisprList *oneList = generateKmers(seq); slAddHead(&listReturn, oneList); totalCrisprs += oneList->crisprCount; elapsedMs = clock1000() - startTime; timingMessage(seq->name, oneList->crisprCount, "crisprs", elapsedMs, "crisprs/sec"); } elapsedMs = clock1000() - scanStart; timingMessage("scanSequence", totalCrisprs, "total crisprs", elapsedMs, "crisprs/sec"); return listReturn; } /* static crisprList *scanSequence(char *inFile) */ -static struct crisprList *rangeExtraction(struct crisprList *all) +static struct crisprList *rangeExtraction(struct crisprList **allReference) /* given ranges in global rangesHash, construct new list of crisprs that * have any type of overlap with the ranges, also extract those items from * the all list. Returns new list. */ { +struct crisprList *all = *allReference; struct crisprList *listReturn = NULL; -struct crisprList *listPtr = NULL; +struct crisprList *list = NULL; int inputChromCount = slCount(all); long long returnListCrisprCount = 0; long long examinedCrisprCount = 0; +struct crisprList *prevChromList = NULL; long elapsedMs = 0; long scanStart = clock1000(); -for (listPtr = all; listPtr; listPtr = listPtr->next) +struct crisprList *nextList = NULL; +for (list = all; list; list = nextList) { + nextList = list->next; // remember before perhaps lost +verbose(1, "# range scan all %p, list %p, nextList %p\n", + (void *)all, (void *)list, (void *)nextList); struct crispr *c = NULL; - struct binKeeper *bk = hashFindVal(rangesHash, listPtr->chrom); + struct binKeeper *bk = hashFindVal(rangesHash, list->chrom); struct crispr *newCrispr = NULL; if (bk != NULL) { struct crispr *prevCrispr = NULL; struct crispr *next = NULL; - for (c = listPtr->chromCrisprs; c; c = next) + for (c = list->chromCrisprs; c; c = next) { ++examinedCrisprCount; struct binElement *hitList = NULL; next = c->next; // remember before perhaps lost int start = c->start; if (c->strand == '-') start += 2; int end = start + 20; hitList = binKeeperFind(bk, start, end); if (hitList) { ++returnListCrisprCount; if (prevCrispr) // remove this one from the all list prevCrispr->next = next; + else + list->chromCrisprs = next; // removing the first one c->next = NULL; slAddHead(&newCrispr, c); // constructing new list - prevCrispr = prevCrispr; } else prevCrispr = c; // remains on all list slFreeList(&hitList); } } if (newCrispr) { struct crisprList *newItem = NULL; AllocVar(newItem); - newItem->chrom = cloneString(listPtr->chrom); - newItem->size = listPtr->size; + newItem->chrom = cloneString(list->chrom); + newItem->size = list->size; newItem->chromCrisprs = newCrispr; newItem->crisprCount = slCount(newCrispr); slAddHead(&listReturn, newItem); +verbose(1, "# range scan newCrispr: %lld crisprs on chrom %s\n", + newItem->crisprCount, newItem->chrom); + if (NULL == list->chromCrisprs) // all have been removed for this chrom + { +verbose(1, "# all crisprs on chrom %s have been removed, prevChromList: %p nextList %p\n", list->chrom, (void *)prevChromList, (void *)nextList); + if (prevChromList) // remove it from the chrom list + prevChromList->next = nextList; + else +{ +verbose(1, "# removing the first chromList, all %p becomes nextList %p\n", (void *)all, (void *)nextList); + all = nextList; // removing the first one +} + } + else + verbose(1, "# range scan same chrom list still has %lld crisprs on chrom %s\n", + (long long)slCount(list->chromCrisprs), list->chrom); } - } // for (listPtr = all; listPtr; listPtr = listPtr->next) + prevChromList = list; + } // for (list = all; list; list = list->next) elapsedMs = clock1000() - scanStart; verbose(1, "# range scan, input %d chromosomes, return %d chromosomes\n", inputChromCount, slCount(listReturn)); timingMessage("range scan", examinedCrisprCount, "examined crisprs", elapsedMs, "crisprs/sec"); timingMessage("range scan", returnListCrisprCount, "returned crisprs", elapsedMs, "crisprs/sec"); +if (NULL == all) + { + allReference = NULL; // they have all been removed +verbose(1, "# range scan, every single chrom has been removed\n"); + } +else if (*allReference != all) + { +verbose(1, "# range scan, first chrom list has been moved from %p to %p\n", (void *)*allReference, (void *)all); + *allReference = all; + } return listReturn; } // static crisprList *rangeExtraction(crisprList *all) +static void queryVsAllArray(struct crisprList *query, + struct crisprList *target) +/* run the query crisprs list against the target list in the array structures */ +{ +struct crisprList *qList = NULL; +long long totalCrisprsQuery = 0; +long long totalCompares = 0; + +long processStart = clock1000(); +long elapsedMs = 0; + +for (qList = query; qList; qList = qList->next) + { + long long qCount = 0; + totalCrisprsQuery += qList->crisprCount; +verbose(1, "# queryVsAllArray %lld query crisprs on chrom %s\n", qList->crisprCount, qList->chrom); + for (qCount = 0; qCount < qList->crisprCount; ++qCount) + { + struct crisprList *tList = NULL; + for (tList = target; tList; tList = tList->next) + { + long long tCount = 0; + totalCompares += tList->crisprCount; +if (0 == qCount) + verbose(1, "# queryVsAllArray %lld target crisprs on chrom %s\n", tList->crisprCount, tList->chrom); + for (tCount = 0; tCount < tList->crisprCount; ++tCount) + { + /* the XOR will determine differences in two sequences + * the shift right 6 removes the PAM sequence + */ + long long misMatch = + (qList->sequence[qCount] ^ tList->sequence[tCount]) >> 6; + if (misMatch) + { + /* possible misMatch bit values: 01 10 11 + * turn those three values into just: 01 + */ + misMatch = (misMatch | (misMatch > 1)) & 0x5555555555; + int bitsOn = _mm_popcnt_u64(misMatch); + if (bitsOn < 5) + { + qList->offBy[bitsOn][qCount] += 1; + tList->offBy[bitsOn][tCount] += 1; + } + } + else + { /* no misMatch, identical crisprs */ + qList->offBy[0][qCount] += 1; + tList->offBy[0][tCount] += 1; + } + } // for (tCount = 0; tCount < tList->crisprCount; ++tCount) + } // for (tList = target; tList; tList = tList->next) + } // for (qCount = 0; qCount < qList->crisprCount; ++qCount) + } // for (qList = query; qList; qList = qList->next) +verbose(1, "# done with scanning, check timing\n"); +elapsedMs = clock1000() - processStart; +timingMessage("queryVsAllArray", totalCrisprsQuery, "crisprs processed", elapsedMs, "crisprs/sec"); +timingMessage("queryVsAllArray", totalCompares, "total comparisons", elapsedMs, "compares/sec"); +} /* static struct crisprList *queryVsAllArray(struct crisprList *query, + struct crisprList *target) */ + +static void allVsAllArray(struct crisprList *all) +/* run this 'all' list vs. itself with arrays */ +{ +struct crisprList *qList = NULL; +long long totalCrisprsQuery = 0; +long long totalCrisprsCompare = 0; + +long processStart = clock1000(); +long elapsedMs = 0; + +/* query runs through all chroms */ +for (qList = all; qList; qList = qList->next) + { + long long qCount = 0; + totalCrisprsQuery += qList->crisprCount; +verbose(1, "# allVsAllArray %lld query crisprs on chrom %s\n", qList->crisprCount, qList->chrom); + /* query runs through all kmers on this chrom */ + for (qCount = 0; qCount < qList->crisprCount; ++qCount) + { + /* target starts on same chrom as query, and + at next kmer after query for this first chrom */ + long long tStart = qCount+1; + struct crisprList *tList = NULL; + for (tList = qList; tList; tList = tList->next) + { + long long tCount = tStart; + totalCrisprsCompare += tList->crisprCount - tStart; + for (tCount = tStart; tCount < tList->crisprCount; ++tCount) + { + /* the XOR will determine differences in two sequences + * the shift right 6 removes the PAM sequence + */ + long long misMatch = + (qList->sequence[qCount] ^ tList->sequence[tCount]) >> 6; + if (misMatch) + { + /* possible misMatch bit values: 01 10 11 + * turn those three values into just: 01 + */ + misMatch = (misMatch | (misMatch > 1)) & 0x5555555555; + int bitsOn = _mm_popcnt_u64(misMatch); + if (bitsOn < 5) + { + qList->offBy[bitsOn][qCount] += 1; + tList->offBy[bitsOn][tCount] += 1; + } + } + else + { /* no misMatch, identical crisprs */ + qList->offBy[0][qCount] += 1; + tList->offBy[0][tCount] += 1; + } + } // for (tCount = 0; tCount < tList->crisprCount; ++tCount) + tStart = 0; /* following chroms run through all */ + } // for (tList = target; tList; tList = tList->next) + } // for (qCount = 0; qCount < qList->crisprCount; ++qCount) + } // for (qList = query; qList; qList = qList->next) +elapsedMs = clock1000() - processStart; +timingMessage("allVsAllArray", totalCrisprsQuery, "crisprs processed", elapsedMs, "crisprs/sec"); +timingMessage("allVsAllArray", totalCrisprsCompare, "total comparisons", elapsedMs, "compares/sec"); +} /* static struct crisprList *allVsAllArray(struct crisprList *query, + struct crisprList *target) */ + +#ifdef NOT static struct crisprList *queryVsAll(struct crisprList *query, struct crisprList *target) /* run the query crisprs list against the target list */ { struct crisprList *listReturn = NULL; long long totalCrisprsQuery = 0; long long totalCompares = 0; int targetChrCount = slCount(target); int queryChrCount = slCount(query); verbose(1, "# queryVsAll: target %d chromosomes vs. query %d chromosomes\n", targetChrCount, queryChrCount); struct crisprList *listPtr = NULL; long processStart = clock1000(); long elapsedMs = 0; for (listPtr = query; listPtr; listPtr = listPtr->next) { struct crispr *c = NULL; totalCrisprsQuery += listPtr->crisprCount; verbose(1, "# queryVsAll: crispr count: %lld on %s\n", listPtr->crisprCount, listPtr->chrom); long long crisprsDone = 0; for (c = listPtr->chromCrisprs; c; c = c->next) { verbose(4, "%s\t%s\t%lld\t%c\n", kmerValToString(c, 0), listPtr->chrom, c->start, c->strand); totalCompares += countOffTargets(listPtr->chrom, c, target); ++crisprsDone; if (crisprsDone < 9) { elapsedMs = clock1000() - processStart; timingMessage("queryVsAll", totalCompares, "total comparisons", elapsedMs, "compares/sec"); } } } // for (listPtr = target; listPtr; listPtr = nextChr) elapsedMs = clock1000() - processStart; timingMessage("queryVsAll", totalCrisprsQuery, "crisprs processed", elapsedMs, "crisprs/sec"); timingMessage("queryVsAll", totalCompares, "total comparisons", elapsedMs, "compares/sec"); return listReturn; -} +} /* static struct crisprList *queryVsAll(struct crisprList *query, + struct crisprList *target) */ + static struct crisprList *allVsAll(struct crisprList *all, struct crisprList *addTo) /* run the all list against itself, add to 'addTo' if given */ { struct crisprList *listReturn = NULL; if (addTo) listReturn = addTo; long long totalCrisprsIn = 0; long long totalCrisprsOut = 0; long long totalCompares = 0; int chrCount = slCount(all); verbose(1, "# allVsAll: crispr list, scanning %d chromosomes, now processing . . .\n", chrCount); struct crisprList *listPtr = NULL; struct crisprList *nextChr = NULL; long processStart = clock1000(); double perSecond = 0.0; long elapsedMs = 0; for (listPtr = all; listPtr; listPtr = nextChr) { struct crispr *newCrispr = NULL; struct crispr *c = NULL; totalCrisprsIn += listPtr->crisprCount; // to verify same in and out verbose(1, "# allVsAll: crispr count: %lld on %s\n", listPtr->crisprCount, listPtr->chrom); struct crispr *next; int crisprsDone = 0; for (c = listPtr->chromCrisprs; c; c = next) { verbose(4, "%s\t%s\t%lld\t%c\n", kmerValToString(c, 0), listPtr->chrom, c->start, c->strand); next = c->next; // remember before lost c->next = NULL; // taking this one out of list listPtr->chromCrisprs = next; // this first item removed from list if ((verboseLevel() > 2) && next) totalCompares += countOffTargets(listPtr->chrom, c, all); slAddHead(&newCrispr, c); // constructing new list ++crisprsDone; elapsedMs = clock1000() - processStart; perSecond = 0.0; if (elapsedMs > 0) perSecond = 1000.0 * crisprsDone / elapsedMs; verbose(1, "# allVsAll: processed %d crisprs @ %ld ms -> %.2f crisprs/sec\n", crisprsDone, elapsedMs, perSecond); verbose(1, "# %d %s:%lld %c %s, offBy0: %d\n", crisprsDone, listPtr->chrom, c->start, c->strand, kmerValToString(c, 0), c->offBy0); perSecond = 0.0; if (elapsedMs > 0) perSecond = 1000.0 * totalCompares / elapsedMs; verbose(1, "# allVsAll: processed %d crisprs total compares %lld @ %ld ms -> %.2f crisprs/sec\n", crisprsDone, totalCompares, elapsedMs, perSecond); } nextChr = listPtr->next; // remember before lost listPtr->next = NULL; // taking out of list listPtr->chromCrisprs = newCrispr; // the new crispr list listPtr->crisprCount = slCount(newCrispr); // the new crispr list totalCrisprsOut += listPtr->crisprCount; // to verify correct all = nextChr; // removes this one from list slAddHead(&listReturn, listPtr); } // for (listPtr = all; listPtr; listPtr = nextChr) if (slCount(listReturn) != chrCount) verbose(1, "#\tERROR: transferred crispr list chrom count %d != beginning count %d\n", slCount(listReturn), chrCount); if (totalCrisprsIn != totalCrisprsOut) verbose(1, "#\tERROR: initial crispr list count %lld != output count %lld\n", totalCrisprsIn, totalCrisprsOut); elapsedMs = clock1000() - processStart; perSecond = 0.0; if (elapsedMs > 0) perSecond = 1000.0 * totalCrisprsIn / elapsedMs; verbose(1, "# %lld total crisprs processed @ %ld ms -> %.2f crisprs/sec\n", totalCrisprsIn, elapsedMs, perSecond); perSecond = 0.0; if (elapsedMs > 0) perSecond = 1000.0 * totalCompares / elapsedMs; verbose(1, "# %lld total comparisons @ %ld ms -> %.2f crisprs/sec\n", totalCompares, elapsedMs, perSecond); return listReturn; } // static struct crisprList *allVsAll(struct crisprList *all, // struct crisprList *addTo) +#endif static struct crisprList *readKmers(char *fileIn) /* read in kmer list from 'fileIn', return list structure */ { verbose(1, "# reading crisprs from: %s\n", fileIn); struct crisprList *listReturn = NULL; struct lineFile *lf = lineFileOpen(fileIn, TRUE); char *row[10]; int wordCount = 0; long long crisprsInput = 0; long startMs = clock1000(); while (0 < (wordCount = lineFileChopNextTab(lf, row, ArraySize(row))) ) { if (3 != wordCount) errAbort("expecing three words at line %d in file %s, found: %d", lf->lineIx, fileIn, wordCount); struct crisprList *newItem = NULL; AllocVar(newItem); newItem->chrom = cloneString(row[0]); newItem->crisprCount = sqlLongLong(row[1]); newItem->size = sqlLongLong(row[2]); newItem->chromCrisprs = NULL; slAddHead(&listReturn, newItem); long long verifyCount = 0; while ( (verifyCount < newItem->crisprCount) && (0 < (wordCount = lineFileChopNextTab(lf, row, ArraySize(row)))) ) { if (3 != wordCount) errAbort("expecing three words at line %d in file %s, found: %d", lf->lineIx, fileIn, wordCount); ++verifyCount; struct crispr *oneCrispr = NULL; AllocVar(oneCrispr); oneCrispr->sequence = sqlLongLong(row[0]); oneCrispr->start = sqlLongLong(row[1]); oneCrispr->strand = row[2][0]; oneCrispr->offBy0 = 0; oneCrispr->offBy1 = 0; oneCrispr->offBy2 = 0; oneCrispr->offBy3 = 0; oneCrispr->offBy4 = 0; slAddHead(&newItem->chromCrisprs, oneCrispr); } if (verifyCount != newItem->crisprCount) errAbort("expecting %lld kmer items at line %d in file %s, found: %lld", newItem->crisprCount, lf->lineIx, fileIn, verifyCount); crisprsInput += verifyCount; } lineFileClose(&lf); long elapsedMs = clock1000() - startMs; timingMessage("readKmers", crisprsInput, "crisprs read in", elapsedMs, "crisprs/sec"); return listReturn; } // static struct crisprList *readKmers(char *fileIn) static void writeKmers(struct crisprList *all, char *fileOut) /* write kmer list 'all' to 'fileOut' */ { FILE *fh = mustOpen(fileOut, "w"); struct crisprList *list = NULL; long long crisprsWritten = 0; long startMs = clock1000(); slReverse(&all); for (list = all; list; list = list->next) { fprintf(fh, "%s\t%lld\t%d\n", list->chrom, list->crisprCount, list->size); struct crispr *c = NULL; slReverse(&list->chromCrisprs); for (c = list->chromCrisprs; c; c = c->next) { fprintf(fh, "%lld\t%lld\t%c\n", c->sequence, c->start, c->strand); ++crisprsWritten; } } carefulClose(&fh); long elapsedMs = clock1000() - startMs; timingMessage("writeKmers", crisprsWritten, "crisprs written", elapsedMs, "crisprs/sec"); } // static void writeKmers(struct crisprList *all, char *fileOut) static void crisprKmers(char *sequence) /* crisprKmers - find and annotate crispr sequences. */ { struct crisprList *queryCrisprs = NULL; -struct crisprList *countedCrisprs = NULL; +// struct crisprList *countedCrisprs = NULL; struct crisprList *allCrisprs = NULL; - if (loadKmers) allCrisprs = readKmers(loadKmers); else allCrisprs = scanSequence(sequence); #ifdef NOT // timing walking through the linked lists long startMs = clock1000(); long long kmerCount = 0; struct crisprList *list = NULL; for (list = allCrisprs; list; list = list->next) kmerCount += slCount(list->chromCrisprs); long elapsedMs = clock1000() - startMs; timingMessage("slCount", kmerCount, "kmers counted", elapsedMs, "kmers/sec"); startMs = clock1000(); slReverse(&allCrisprs); for (list = allCrisprs; list; list = list->next) slReverse(&list->chromCrisprs); elapsedMs = clock1000() - startMs; timingMessage("slReverse", kmerCount, "kmers reversed", elapsedMs, "kmers/sec"); return; #endif if (dumpKmers) { writeKmers(allCrisprs, dumpKmers); return; } /* processing those crisprs */ if (verboseLevel() > 1) { /* if ranges have been specified, construct queryList of kmers to measure */ if (rangesHash) { - queryCrisprs = rangeExtraction(allCrisprs); - /* first run up query vs. all, no list mucking about */ + /* result here is two exclusive sets: query, and allCrisprs + * the query crisprs have been extracted from the allCrisprs */ +verbose(1, "# before rangeExtraction, allCrisprs: %p\n", (void *)allCrisprs); + queryCrisprs = rangeExtraction(& allCrisprs); +verbose(1, "# after rangeExtraction, allCrisprs: %p\n", (void *)allCrisprs); +verbose(1, "# copyToArray(queryCrisprs)\n"); + copyToArray(queryCrisprs); + if (allCrisprs) // if there are any left on the all list + { +verbose(1, "# copyToArray(allCrisprs)\n"); + copyToArray(allCrisprs); + /* first run up query vs. all */ + queryVsAllArray(queryCrisprs, allCrisprs); + } + /* then run up the query vs. itself avoiding self vs. self */ + allVsAllArray(queryCrisprs); + showCountsArray(queryCrisprs); +verbose(1, "# back from showCountsArray\n"); +#ifdef NOT countedCrisprs = queryVsAll(queryCrisprs, allCrisprs); /* then run up query vs. itself, add to countedCrisprs */ countedCrisprs = allVsAll(queryCrisprs, countedCrisprs); +#endif + } + else + { + copyToArray(allCrisprs); + /* run up all vs. all avoiding self vs. self */ + allVsAllArray(allCrisprs); + showCountsArray(allCrisprs); } +#ifdef NOT else countedCrisprs = allVsAll(allCrisprs, NULL); +#endif +#ifdef NOT showCounts(countedCrisprs); +#endif } +verbose(1, "# returning from crisprKmers\n"); } // static void crisprKmers(char *sequence) int main(int argc, char *argv[]) /* Process command line, initialize translation arrays and call the process */ { optionInit(&argc, argv, options); if (argc != 2) usage(); +verbose(0, "# running verboseLevel: %d\n", verboseLevel()); + bedFileOut = optionVal("bed", bedFileOut); dumpKmers = optionVal("dumpKmers", dumpKmers); loadKmers = optionVal("loadKmers", loadKmers); ranges = optionVal("ranges", ranges); if (ranges) rangesHash = readRanges(ranges); initOrderedNtVal(); /* set up orderedNtVal[] */ crisprKmers(argv[1]); +verbose(1, "# returned from crisprKmers(%s}\n", argv[1]); +verbose(1, "# checking heap after crisprKmers\n"); if (verboseLevel() > 1) printVmPeak(); return 0; }