26c2f650359cc1c74fb31d96109bc0f8dedbc3d7 angie Thu May 30 10:32:19 2019 -0700 Adding BAM and VCF item counts to hubApi's list/tracks function. Note: older index files may not contain counts. refs #18869, #23521 diff --git src/inc/bamFile.h src/inc/bamFile.h index d11dc14..5da2dd1 100644 --- src/inc/bamFile.h +++ src/inc/bamFile.h @@ -1,173 +1,180 @@ /* bamFile -- interface to binary alignment format files using Heng Li's samtools lib. */ #ifndef BAMFILE_H #define BAMFILE_H #include "dnaseq.h" #include "dystring.h" // bam.h is incomplete without _IOLIB set to 1, 2 or 3. 2 is used by Makefile.generic: #ifndef _IOLIB #define _IOLIB 2 #endif #include "htslib/sam.h" typedef samFile samfile_t; typedef hts_idx_t bam_index_t; typedef bam_hdr_t bam_header_t; typedef int (*bam_fetch_f)(const bam1_t *bam, void *data, bam_hdr_t *header) ; #define samopen(a,b,c) sam_open(a,b) #define samclose(a) sam_close(a) #define bam1_qname bam_get_qname #define bam1_qual bam_get_qual #define bam1_aux bam_get_aux #define bam1_cigar bam_get_cigar #define bam1_seq bam_get_seq #define bam1_seqi bam_seqi #define bam_nt16_rev_table seq_nt16_str #define data_len l_data boolean bamFileExists(char *bamFileName); /* Return TRUE if we can successfully open the bam file and its index file. */ void bamFileAndIndexMustExist(char *fileOrUrl, char *baiFileOrUrl); /* Open both a bam file and its accompanying index or errAbort; this is what it * takes for diagnostic info to propagate up through errCatches in calling code. * The parameter baiFileOrUrl can be NULL, defaults of <fileOrUrl>.bai. */ samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName); /* Return an open bam file as well as the filename of the bam. */ samfile_t *bamMustOpenLocal(char *fileName, char *mode, void *extraHeader); /* Open up sam or bam file or die trying. The mode parameter is * "r" - open SAM to read * "rb" - open BAM to read * "w" - open SAM to write * "wb" - open BAM to write * The extraHeader is generally NULL in the read case, and the write case * contains a pointer to a bam_header_t with information about the header. * The implementation is just a wrapper around samopen from the samtools library * that aborts with error message if there's a problem with the open. */ +long long bamFileItemCount(char *fileOrUrl, char *baiFileOrUrl); +/* Return the total number of mapped items across all sequences in fileOrUrl, using index file. + * If baiFileOrUrl is NULL, the index file is assumed to be fileOrUrl.bai. + * NOTE: not all bam index files include mapped item counts, so this may return 0 even for large + * bam. As of May 2019, our copy of hts_idx_get_stat does not support cram indexes + * (perhaps they never include counts?), so this always returns 0 for cram. */ + void bamFetchAlreadyOpen(samfile_t *samfile, bam_hdr_t *header, bam_index_t *idx, char *bamFileName, char *position, bam_fetch_f callbackFunc, void *callbackData); /* With the open bam file, return items the same way with the callbacks as with bamFetch() */ /* except in this case use an already-open bam file and index (use bam_index_load and free() for */ /* the index). It seems a little strange to pass the filename in with the open bam, but */ /* it's just used to report errors. */ void bamAndIndexFetchPlus(char *fileOrUrl, char *baiFileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData, samfile_t **pSamFile, char *refUrl, char *cacheDir); /* Open the .bam file with the .bai index specified by baiFileOrUrl. * baiFileOrUrl can be NULL and defaults to <fileOrUrl>.bai. * 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. */ void bamFetchPlus(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData, samfile_t **pSamFile, char *refUrl, char *cacheDir); /* 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. * refUrl points to the place to grab CRAM reference sequences (if any) * cacheDir points to the directory in which CRAM reference sequences are cached */ void bamFetch(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData, samfile_t **pSamFile); /* 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. */ void bamClose(samfile_t **pSamFile); /* Close down a samefile_t */ boolean bamIsRc(const bam1_t *bam); /* Return TRUE if alignment is on - strand. */ INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp) /* Given an unsigned int containing a number of bases and an offset into an * array of BAM-enhanced-CIGAR ASCII characters (operations), store operation * char into *retOp (retOp must not be NULL) and return the number of bases. */ { // decoding lifted from samtools bam.c bam_format1_core(), long may it remain stable: #define BAM_DOT_C_OPCODE_STRING "MIDNSHP=X" int n = packed>>BAM_CIGAR_SHIFT; int opcode = packed & BAM_CIGAR_MASK; if (opcode >= strlen(BAM_DOT_C_OPCODE_STRING)) errAbort("bamUnpackCigarElement: unrecognized opcode %d. " "(I only recognize 0..%lu [" BAM_DOT_C_OPCODE_STRING "]) " "Perhaps samtools bam.c's bam_format1 encoding changed? If so, update me.", opcode, (unsigned long)(strlen(BAM_DOT_C_OPCODE_STRING)-1)); *retOp = BAM_DOT_C_OPCODE_STRING[opcode]; return n; } 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). */ 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. */ 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. */ UBYTE *bamGetQueryQuals(const bam1_t *bam, boolean useStrand); /* Return the base quality scores encoded in bam as an array of ubytes. */ void bamUnpackCigar(const bam1_t *bam, struct dyString *dyCigar); /* Unpack CIGAR string into dynamic string */ char *bamGetCigar(const bam1_t *bam); /* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */ void bamShowCigarEnglish(const bam1_t *bam); /* Print out cigar in English e.g. "20 (mis)Match, 1 Deletion, 3 (mis)Match" */ void bamShowFlagsEnglish(const bam1_t *bam); /* Print out flags in English, e.g. "Mate is on '-' strand; Properly paired". */ int bamGetTargetLength(const bam1_t *bam); /* Tally up the alignment's length on the reference sequence from * bam's packed-int CIGAR representation. */ bam1_t *bamClone(const bam1_t *bam); /* Return a newly allocated copy of bam. */ void bamShowTags(const bam1_t *bam); /* Print out tags in HTML: bold key, no type indicator for brevity. */ 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. */ void bamUnpackAux(const bam1_t *bam, struct dyString *dy); /* Unpack the tag:type:val part of bam into dy */ void samToBed(char *samIn, char *bedOut); /* samToBed - Convert SAM file to a pretty simple minded bed file.. */ void samToOpenBed(char *samIn, FILE *f); /* Like samToOpenBed, but the output is the already open file f. */ struct psl *bamToPslUnscored(const bam1_t *bam, const bam_hdr_t *hdr); /* Translate BAM's numeric CIGAR encoding into PSL sufficient for cds.c (just coords, * no scoring info) */ #endif//ndef BAMFILE_H