d2c7e8be3ceae6027a5274faafdf6239d778cc63 aamp Sat Jul 16 08:31:16 2011 -0700 Changes related to change source filenames around: bamUdc.ch -> bamFile.ch and bamFile.ch -> hgBam.ch diff --git src/lib/bamUdc.c src/lib/bamUdc.c deleted file mode 100644 index 60dfc86..0000000 --- src/lib/bamUdc.c +++ /dev/null @@ -1,693 +0,0 @@ -/* bamFile -- interface to binary alignment format files using Heng Li's samtools lib. */ - -#include "common.h" -#include "portable.h" -#include "bamUdc.h" -#ifdef USE_BAM -#include "htmshell.h" -#include "udc.h" - -static boolean isRegularFile(char *filename) -/* File not only exists, but is also a file not a directory. */ -{ -struct stat mystat; -if (stat(filename, &mystat) != 0) - return FALSE; -return S_ISREG(mystat.st_mode); -} - -static char *samtoolsFileNameUdcFuse(char *fileOrUrl, char *udcFuseRoot) -/* If udcFuse is configured, and we have a URL, convert it into a filename in - * the udcFuse filesystem for use by samtools. Thus samtools will think it's - * working on a local file, but udcFuse will pass access requests to udc and - * we'll get the benefits of sparse-file local caching and https support. - * udcFuse needs us to open udc files before invoking udcFuse paths, so open - * both the .bam and .bai (index) URLs with udc here. - * If udcFuse is not configured, or fileOrUrl is not an URL, just pass through fileOrUrl. */ -{ -char *protocol = NULL, *afterProtocol = NULL, *colon = NULL, *auth = NULL; -udcParseUrlFull(fileOrUrl, &protocol, &afterProtocol, &colon, &auth); -if (udcFuseRoot != NULL && afterProtocol != NULL) - { - struct dyString *dy = dyStringNew(0); - if (auth == NULL) - auth = ""; - dyStringPrintf(dy, "%s/%s/%s%s", udcFuseRoot, protocol, auth, afterProtocol); - char *bamFileName = dyStringCannibalize(&dy); - if (!isRegularFile(bamFileName)) - { - verbose(2, "going to call udcFileMayOpen(%s).\n", fileOrUrl); - struct udcFile *udcf = udcFileMayOpen(fileOrUrl, NULL); - if (udcf != NULL) - { - udcFileClose(&udcf); - verbose(2, "closed udcf. testing existence of %s.\n", bamFileName); - if (!isRegularFile(bamFileName)) - { - warn("Cannot find %s -- remount udcFuse?", bamFileName); - freeMem(bamFileName); - return cloneString(fileOrUrl); - } - } - else - { - warn("Failed to open BAM URL \"%s\" with udc", fileOrUrl); - freeMem(bamFileName); - return cloneString(fileOrUrl); - } - } - // Look for index file: xxx.bam.bai or xxx.bai. Look for both in udcFuse, - // and only open the URL with udc if neither udcFuse file exists. - int urlLen = strlen(fileOrUrl), fLen = strlen(bamFileName); - char *indexFileName = needMem(fLen+5); - safef(indexFileName, fLen+5, "%s.bai", bamFileName); - if (!isRegularFile(indexFileName)) - { - verbose(2, "%s does not already exist\n", indexFileName); - char *altIndexFileName = NULL; - if (endsWith(fileOrUrl, ".bam")) - { - altIndexFileName = cloneString(indexFileName); - strcpy(altIndexFileName+fLen-1, "i"); - } - if (!(altIndexFileName && isRegularFile(altIndexFileName))) - { - char *indexUrl = needMem(urlLen+5); - safef(indexUrl, urlLen+5, "%s.bai", fileOrUrl); - verbose(2, "going to call udcFileMayOpen(%s).\n", indexUrl); - struct udcFile *udcf = udcFileMayOpen(indexUrl, NULL); - if (udcf != NULL) - udcFileClose(&udcf); - else if (altIndexFileName != NULL) - { - char *altIndexUrl = cloneString(indexUrl); - strcpy(altIndexUrl+urlLen-1, "i"); - verbose(2, "going to call udcFileMayOpen(%s).\n", altIndexUrl); - udcf = udcFileMayOpen(altIndexUrl, NULL); - if (udcf == NULL) - { - warn("Cannot find BAM index file (%s or %s)", indexUrl, altIndexUrl); - return cloneString(fileOrUrl); - } - udcFileClose(&udcf); - freeMem(altIndexUrl); - } - else - { - warn("Cannot find BAM index file for \"%s\"", fileOrUrl); - return cloneString(fileOrUrl); - } - freeMem(indexUrl); - } - freeMem(altIndexFileName); - } - freeMem(indexFileName); - return bamFileName; - } -return cloneString(fileOrUrl); -} - -#ifndef KNETFILE_HOOKS -static char *getSamDir() -/* Return the name of a trash dir for samtools to run in (it creates files in current dir) - * and make sure the directory exists. */ -{ -static char *samDir = NULL; -char *dirName = "samtools"; -if (samDir == NULL) - { - mkdirTrashDirectory(dirName); - size_t len = strlen(trashDir()) + 1 + strlen(dirName) + 1; - samDir = needMem(len); - safef(samDir, len, "%s/%s", trashDir(), dirName); - } -return samDir; -} -#endif//ndef KNETFILE_HOOKS - -boolean bamFileExistsUdc(char *fileOrUrl, char *udcFuseRoot) -/* Return TRUE if we can successfully open the bam file and its index file. */ -{ -char *bamFileName = samtoolsFileNameUdcFuse(fileOrUrl, udcFuseRoot); -samfile_t *fh = samopen(bamFileName, "rb", NULL); -boolean usingUrl = TRUE; -usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://")); -if (fh != NULL) - { -#ifndef KNETFILE_HOOKS - // When file is an URL, this caches the index file in addition to validating: - // Since samtools's url-handling code saves the .bai file to the current directory, - // chdir to a trash directory before calling bam_index_load, then chdir back. - char *runDir = getCurrentDir(); - char *samDir = getSamDir(); - if (usingUrl) - setCurrentDir(samDir); -#endif//ndef KNETFILE_HOOKS - bam_index_t *idx = bam_index_load(bamFileName); -#ifndef KNETFILE_HOOKS - if (usingUrl) - setCurrentDir(runDir); -#endif//ndef KNETFILE_HOOKS - samclose(fh); - if (idx == NULL) - { - warn("bamFileExists: failed to read index corresponding to %s", bamFileName); - return FALSE; - } - free(idx); // Not freeMem, freez etc -- sam just uses malloc/calloc. - return TRUE; - } -return FALSE; -} - -samfile_t *bamOpenUdc(char *fileOrUrl, char **retBamFileName, char *udcFuseRoot) -/* Return an open bam file, dealing with FUSE caching if need be. - * Return parameter if NON-null will return the file name after FUSing */ -{ -char *bamFileName = samtoolsFileNameUdcFuse(fileOrUrl, udcFuseRoot); -if (retBamFileName != NULL) - *retBamFileName = bamFileName; -samfile_t *fh = samopen(bamFileName, "rb", NULL); -if (fh == NULL) - { - boolean usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://")); - struct dyString *urlWarning = dyStringNew(0); - if (usingUrl) - { - boolean usingUdc = (udcFuseRoot != NULL && startsWith(udcFuseRoot, bamFileName)); - if (usingUdc) - dyStringAppend(urlWarning, " (using udcFuse)"); - dyStringAppend(urlWarning, - ". If you are able to access the URL with your web browser, " - "please try reloading this page."); - } - errAbort("Failed to open %s%s", fileOrUrl, urlWarning->string); - } -return fh; -} - -void bamClose(samfile_t **pSamFile) -/* Close down a samefile_t */ -{ -if (pSamFile != NULL) - { - samclose(*pSamFile); - *pSamFile = NULL; - } -} - -void bamFetchUdc(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData, - samfile_t **pSamFile, char *udcFuseRoot) -/* Open the .bam file, fetch items in the seq:start-end position range, - * and call callbackFunc on each bam item retrieved from the file plus callbackData. - * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. - * The pSamFile parameter is optional. If non-NULL it will be filled in, just for - * the benefit of the callback function, with the open samFile. */ -{ -char *bamFileName = NULL; -samfile_t *fh = bamOpenUdc(fileOrUrl, &bamFileName, udcFuseRoot); -boolean usingUrl = TRUE; -usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://")); -if (pSamFile != NULL) - *pSamFile = fh; -int chromId, start, end; -int ret = bam_parse_region(fh->header, position, &chromId, &start, &end); -if (ret != 0 && startsWith("chr", position)) - ret = bam_parse_region(fh->header, position+strlen("chr"), &chromId, &start, &end); -if (ret != 0) - // If the bam file does not cover the current chromosome, OK - return; -#ifndef KNETFILE_HOOKS -// Since samtools' url-handling code saves the .bai file to the current directory, -// chdir to a trash directory before calling bam_index_load, then chdir back. -char *runDir = getCurrentDir(); -char *samDir = getSamDir(); -if (usingUrl) - setCurrentDir(samDir); -#endif//ndef KNETFILE_HOOKS -bam_index_t *idx = bam_index_load(bamFileName); -#ifndef KNETFILE_HOOKS -if (usingUrl) - setCurrentDir(runDir); -#endif//ndef KNETFILE_HOOKS -if (idx == NULL) - warn("bam_index_load(%s) failed.", bamFileName); -else - { - ret = bam_fetch(fh->x.bam, idx, chromId, start, end, callbackData, callbackFunc); - if (ret != 0) - warn("bam_fetch(%s, %s (chromId=%d) failed (%d)", bamFileName, position, chromId, ret); - free(idx); // Not freeMem, freez etc -- sam just uses malloc/calloc. - } -bamClose(&fh); -} - -boolean bamIsRc(const bam1_t *bam) -/* Return TRUE if alignment is on - strand. */ -{ -const bam1_core_t *core = &bam->core; -return (core->flag & BAM_FREVERSE); -} - -void bamGetSoftClipping(const bam1_t *bam, int *retLow, int *retHigh, int *retClippedQLen) -/* If retLow is non-NULL, set it to the number of "soft-clipped" (skipped) bases at - * the beginning of the query sequence and quality; likewise for retHigh at end. - * For convenience, retClippedQLen is the original query length minus soft clipping - * (and the length of the query sequence that will be returned). */ -{ -unsigned int *cigarPacked = bam1_cigar(bam); -const bam1_core_t *core = &bam->core; -char op; -int n = bamUnpackCigarElement(cigarPacked[0], &op); -int low = (op == 'S') ? n : 0; -n = bamUnpackCigarElement(cigarPacked[core->n_cigar-1], &op); -int high = (op == 'S') ? n : 0; -if (retLow != NULL) - *retLow = low; -if (retHigh != NULL) - *retHigh = high; -if (retClippedQLen != NULL) - *retClippedQLen = (core->l_qseq - low - high); -} - - -void bamUnpackQuerySequence(const bam1_t *bam, boolean useStrand, char *qSeq) -/* Fill in qSeq with the nucleotide sequence encoded in bam. The BAM format - * reverse-complements query sequence when the alignment is on the - strand, - * so if useStrand is given we rev-comp it back to restore the original query - * sequence. */ -{ -const bam1_core_t *core = &bam->core; -int qLen = core->l_qseq; -uint8_t *packedQSeq = bam1_seq(bam); -int i; -for (i = 0; i < qLen; i++) - qSeq[i] = bam_nt16_rev_table[bam1_seqi(packedQSeq, i)]; -qSeq[i] = '\0'; -if (useStrand && bamIsRc(bam)) - reverseComplement(qSeq, qLen); -} - -char *bamGetQuerySequence(const bam1_t *bam, boolean useStrand) -/* Allocate and return the nucleotide sequence encoded in bam. The BAM format - * reverse-complements query sequence when the alignment is on the - strand, - * so if useStrand is given we rev-comp it back to restore the original query - * sequence. */ -{ -const bam1_core_t *core = &bam->core; -int qLen = core->l_qseq; -char *qSeq = needMem(qLen+1); -bamUnpackQuerySequence(bam, useStrand, qSeq); -return qSeq; -} - -UBYTE *bamGetQueryQuals(const bam1_t *bam, boolean useStrand) -/* Return the base quality scores encoded in bam as an array of ubytes. */ -{ -const bam1_core_t *core = &bam->core; -int qLen = core->l_qseq; -UBYTE *arr = needMem(qLen); -boolean isRc = useStrand && bamIsRc(bam); -UBYTE *qualStr = bam1_qual(bam); -int i; -for (i = 0; i < core->l_qseq; i++) - { - int offset = isRc ? (qLen - 1 - i) : i; - arr[i] = (qualStr[0] == 255) ? 255 : qualStr[offset]; - } -return arr; -} - -void bamUnpackCigar(const bam1_t *bam, struct dyString *dyCigar) -/* Unpack CIGAR string into dynamic string */ -{ -unsigned int *cigarPacked = bam1_cigar(bam); -const bam1_core_t *core = &bam->core; -int i; -for (i = 0; i < core->n_cigar; i++) - { - char op; - int n = bamUnpackCigarElement(cigarPacked[i], &op); - dyStringPrintf(dyCigar, "%d", n); - dyStringAppendC(dyCigar, op); - } -} - -char *bamGetCigar(const bam1_t *bam) -/* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */ -{ -const bam1_core_t *core = &bam->core; -struct dyString *dyCigar = dyStringNew(min(8, core->n_cigar*4)); -bamUnpackCigar(bam, dyCigar); -return dyStringCannibalize(&dyCigar); -} - -void bamShowCigarEnglish(const bam1_t *bam) -/* Print out cigar in English e.g. "20 (mis)Match, 1 Deletion, 3 (mis)Match" */ -{ -unsigned int *cigarPacked = bam1_cigar(bam); -const bam1_core_t *core = &bam->core; -int i; -for (i = 0; i < core->n_cigar; i++) - { - char op; - int n = bamUnpackCigarElement(cigarPacked[i], &op); - if (i > 0) - printf(", "); - switch (op) - { - case 'M': // match or mismatch (gapless aligned block) - printf("%d (mis)Match", n); - break; - case 'I': // inserted in query - printf("%d Insertion", n); - break; - case 'S': // skipped query bases at beginning or end ("soft clipping") - printf("%d Skipped", n); - break; - case 'D': // deleted from query - printf("%d Deletion", n); - break; - case 'N': // long deletion from query (intron as opposed to small del) - printf("%d deletioN", n); - break; - case 'H': // skipped query bases not stored in record's query sequence ("hard clipping") - printf("%d Hard clipped query", n); - break; - case 'P': // P="silent deletion from padded reference sequence" - printf("%d Padded / silent deletion", n); - break; - default: - errAbort("bamShowCigarEnglish: unrecognized CIGAR op %c -- update me", op); - } - } -} - -static void descFlag(unsigned flag, unsigned bitMask, char *desc, boolean makeRed, - boolean *retFirst) -/* Describe a flag bit (or multi-bit mask) if it is set in flag. */ -{ -if ((flag & bitMask) == bitMask) // *all* bits in bitMask are set in flag - { - if (!*retFirst) - printf(" | "); - printf("<span%s>(<TT>0x%02x</TT>) %s</span>", - (makeRed ? " style='color: red'" : ""), bitMask, desc); - *retFirst = FALSE; - } -} - -void bamShowFlagsEnglish(const bam1_t *bam) -/* Print out flags in English, e.g. "Mate is on '-' strand; Properly paired". */ -{ -const bam1_core_t *core = &bam->core; -unsigned flag = core->flag; -boolean first = TRUE; -descFlag(flag, BAM_FDUP, "Optical or PCR duplicate", TRUE, &first); -descFlag(flag, BAM_FQCFAIL, "QC failure", TRUE, &first); -descFlag(flag, BAM_FSECONDARY, "Not primary alignment", TRUE, &first); -descFlag(flag, BAM_FREAD2, "Read 2 of pair", FALSE, &first); -descFlag(flag, BAM_FREAD1, "Read 1 of pair", FALSE, &first); -descFlag(flag, BAM_FMREVERSE, "Mate is on '-' strand", FALSE, &first); -descFlag(flag, BAM_FREVERSE, "Read is on '-' strand", FALSE, &first); -descFlag(flag, BAM_FMUNMAP, "Mate is unmapped", TRUE, &first); -if (flag & BAM_FUNMAP) - errAbort("Read is unmapped (what is it doing here?!?)"); -descFlag(flag, (BAM_FPROPER_PAIR | BAM_FPAIRED), "Properly paired", FALSE, &first); -if ((flag & BAM_FPAIRED) && !(flag & BAM_FPROPER_PAIR)) - descFlag(flag, BAM_FPAIRED, "Not properly paired", TRUE, &first); -} - -int bamGetTargetLength(const bam1_t *bam) -/* Tally up the alignment's length on the reference sequence from - * bam's packed-int CIGAR representation. */ -{ -unsigned int *cigarPacked = bam1_cigar(bam); -const bam1_core_t *core = &bam->core; -int tLength=0; -int i; -for (i = 0; i < core->n_cigar; i++) - { - char op; - int n = bamUnpackCigarElement(cigarPacked[i], &op); - switch (op) - { - case 'M': // match or mismatch (gapless aligned block) - tLength += n; - break; - case 'I': // inserted in query - break; - case 'D': // deleted from query - case 'N': // long deletion from query (intron as opposed to small del) - tLength += n; - break; - case 'S': // skipped query bases at beginning or end ("soft clipping") - case 'H': // skipped query bases not stored in record's query sequence ("hard clipping") - case 'P': // P="silent deletion from padded reference sequence" -- ignore these. - break; - default: - errAbort("bamGetTargetLength: unrecognized CIGAR op %c -- update me", op); - } - } -return tLength; -} - -bam1_t *bamClone(const bam1_t *bam) -/* Return a newly allocated copy of bam. */ -{ -// Using typecasts to get around compiler complaints about bam being const: -bam1_t *newBam = cloneMem((void *)bam, sizeof(*bam)); -newBam->data = cloneMem((void *)bam->data, bam->data_len*sizeof(bam->data[0])); -return newBam; -} - -void bamShowTags(const bam1_t *bam) -/* Print out tags in HTML: bold key, no type indicator for brevity. */ -{ -// adapted from part of bam.c bam_format1: -uint8_t *s = bam1_aux(bam); -while (s < bam->data + bam->data_len) - { - uint8_t type, key[2]; - key[0] = s[0]; key[1] = s[1]; - s += 2; type = *s; ++s; - printf(" <B>%c%c</B>:", key[0], key[1]); - if (type == 'A') { printf("%c", *s); ++s; } - else if (type == 'C') { printf("%u", *s); ++s; } - else if (type == 'c') { printf("%d", *s); ++s; } - else if (type == 'S') { printf("%u", *(uint16_t*)s); s += 2; } - else if (type == 's') { printf("%d", *(int16_t*)s); s += 2; } - else if (type == 'I') { printf("%u", *(uint32_t*)s); s += 4; } - else if (type == 'i') { printf("%d", *(int32_t*)s); s += 4; } - else if (type == 'f') { printf("%g", *(float*)s); s += 4; } - else if (type == 'd') { printf("%lg", *(double*)s); s += 8; } - else if (type == 'Z' || type == 'H') - { - htmTextOut(stdout, (char *)s); - s += strlen((char *)s) + 1; - } - } -putc('\n', stdout); -} - -char *bamGetTagString(const bam1_t *bam, char *tag, char *buf, size_t bufSize) -/* If bam's tags include the given 2-character tag, place the value into - * buf (zero-terminated, trunc'd if nec) and return a pointer to buf, - * or NULL if tag is not present. */ -{ -if (tag == NULL) - errAbort("NULL tag passed to bamGetTagString"); -if (! (isalpha(tag[0]) && isalnum(tag[1]) && tag[2] == '\0')) - errAbort("bamGetTagString: invalid tag '%s'", htmlEncode(tag)); -char *val = NULL; -// adapted from part of bam.c bam_format1: -uint8_t *s = bam1_aux(bam); -while (s < bam->data + bam->data_len) - { - uint8_t type, key[2]; - key[0] = s[0]; key[1] = s[1]; - s += 2; type = *s; ++s; - if (key[0] == tag[0] && key[1] == tag[1]) - { - if (type == 'A') { snprintf(buf, bufSize, "%c", *s);} - else if (type == 'C') { snprintf(buf, bufSize, "%u", *s); } - else if (type == 'c') { snprintf(buf, bufSize, "%d", *s); } - else if (type == 'S') { snprintf(buf, bufSize, "%u", *(uint16_t*)s); } - else if (type == 's') { snprintf(buf, bufSize, "%d", *(int16_t*)s); } - else if (type == 'I') { snprintf(buf, bufSize, "%u", *(uint32_t*)s); } - else if (type == 'i') { snprintf(buf, bufSize, "%d", *(int32_t*)s); } - else if (type == 'f') { snprintf(buf, bufSize, "%g", *(float*)s); } - else if (type == 'd') { snprintf(buf, bufSize, "%lg", *(double*)s); } - else if (type == 'Z' || type == 'H') strncpy(buf, (char *)s, bufSize); - else buf[0] = '\0'; - buf[bufSize-1] = '\0'; // TODO: is this nec?? see man pages - val = buf; - break; - } - else - { - if (type == 'A' || type == 'C' || type == 'c') { ++s; } - else if (type == 'S' || type == 's') { s += 2; } - else if (type == 'I' || type == 'i' || type == 'f') { s += 4; } - else if (type == 'd') { s += 8; } - else if (type == 'Z' || type == 'H') - { - while (*s++); - } - } - } -return val; -} - -void bamUnpackAux(const bam1_t *bam, struct dyString *dy) -/* Unpack the tag:type:val part of bam into dy */ -{ -// adapted from part of bam.c bam_format1: -uint8_t *s = bam1_aux(bam); -boolean firstTime = TRUE; -while (s < bam->data + bam->data_len) - { - if (firstTime) - firstTime = FALSE; - else - dyStringAppendC(dy, '\t'); - dyStringAppendC(dy, *s++); - dyStringAppendC(dy, *s++); - dyStringAppendC(dy, ':'); - dyStringAppendC(dy, s[0]); - dyStringAppendC(dy, ':'); - uint8_t type = *s++; - if (type == 'A') { dyStringPrintf(dy, "%c", *s); ++s; } - else if (type == 'C') { dyStringPrintf(dy, "%u", *s); ++s; } - else if (type == 'c') { dyStringPrintf(dy, "%d", *s); ++s; } - else if (type == 'S') { dyStringPrintf(dy, "%u", *(uint16_t*)s); s += 2; } - else if (type == 's') { dyStringPrintf(dy, "%d", *(int16_t*)s); s += 2; } - else if (type == 'I') { dyStringPrintf(dy, "%u", *(uint32_t*)s); s += 4; } - else if (type == 'i') { dyStringPrintf(dy, "%d", *(int32_t*)s); s += 4; } - else if (type == 'f') { dyStringPrintf(dy, "%g", *(float*)s); s += 4; } - else if (type == 'd') { dyStringPrintf(dy, "%lg", *(double*)s); s += 8; } - else if (type == 'Z' || type == 'H') - { - dyStringAppend(dy, (char *)s); - s += strlen((char *)s) + 1; - } - } -} - -#else -// If we're not compiling with samtools, make stub routines so compile won't fail: - -boolean bamFileExistsUdcFuse(char *bamFileName, char *udcFuseRoot) -/* Return TRUE if we can successfully open the bam file and its index file. */ -{ -warn(COMPILE_WITH_SAMTOOLS, "bamFileExistsUdcFuse"); -return FALSE; -} - -samfile_t *bamOpenUdcFuse(char *fileOrUrl, char **retBamFileName) -/* Return an open bam file, dealing with some FUSE caching if need be. */ -{ -warn(COMPILE_WITH_SAMTOOLS, "bamOpenUdc"); -return FALSE; -} - -void bamClose(samfile_t **pSamFile) -/* Close down a samefile_t */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamClose"); -} - -void bamFetchUdcFuse(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData, - samfile_t **pSamFile, char *udcFuseRoot) -/* Open the .bam file, fetch items in the seq:start-end position range, - * and call callbackFunc on each bam item retrieved from the file plus callbackData. - * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. - * The pSamFile parameter is optional. If non-NULL it will be filled in, just for - * the benefit of the callback function, with the open samFile. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamFetch"); -} - -boolean bamIsRc(const bam1_t *bam) -/* Return TRUE if alignment is on - strand. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamIsRc"); -return FALSE; -} - -void bamGetSoftClipping(const bam1_t *bam, int *retLow, int *retHigh, int *retClippedQLen) -/* If retLow is non-NULL, set it to the number of "soft-clipped" (skipped) bases at - * the beginning of the query sequence and quality; likewise for retHigh at end. - * For convenience, retClippedQLen is the original query length minus soft clipping - * (and the length of the query sequence that will be returned). */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamGetSoftClipping"); -} - -char *bamGetQuerySequence(const bam1_t *bam, boolean useStrand) -/* Return the nucleotide sequence encoded in bam. The BAM format - * reverse-complements query sequence when the alignment is on the - strand, - * so if useStrand is given we rev-comp it back to restore the original query - * sequence. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamGetQuerySequence"); -return NULL; -} - -UBYTE *bamGetQueryQuals(const bam1_t *bam, boolean useStrand) -/* Return the base quality scores encoded in bam as an array of ubytes. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamGetQueryQuals"); -return NULL; -} - -char *bamGetCigar(const bam1_t *bam) -/* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamGetCigar"); -return NULL; -} - -void bamShowCigarEnglish(const bam1_t *bam) -/* Print out cigar in English e.g. "20 (mis)Match, 1 Deletion, 3 (mis)Match" */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamShowCigarEnglish"); -} - -void bamShowFlagsEnglish(const bam1_t *bam) -/* Print out flags in English, e.g. "Mate is on '-' strand; Properly paired". */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamShowFlagsEnglish"); -} - -int bamGetTargetLength(const bam1_t *bam) -/* Tally up the alignment's length on the reference sequence from - * bam's packed-int CIGAR representation. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamGetTargetLength"); -return 0; -} - -bam1_t *bamClone(const bam1_t *bam) -/* Return a newly allocated copy of bam. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamClone"); -return NULL; -} - -void bamShowTags(const bam1_t *bam) -/* Print out tags in HTML: bold key, no type indicator for brevity. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamShowTags"); -} - -char *bamGetTagString(const bam1_t *bam, char *tag, char *buf, size_t bufSize) -/* If bam's tags include the given 2-character tag, place the value into - * buf (zero-terminated, trunc'd if nec) and return a pointer to buf, - * or NULL if tag is not present. */ -{ -errAbort(COMPILE_WITH_SAMTOOLS, "bamGetTagString"); -return NULL; -} - -#endif//ndef USE_BAM