src/hg/lib/bamFile.c 1.7

Index: src/hg/lib/bamFile.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/bamFile.c,v
retrieving revision 1.6
retrieving revision 1.7
diff -b -B -U 1000000 -r1.6 -r1.7
--- src/hg/lib/bamFile.c	24 Aug 2009 23:47:56 -0000	1.6
+++ src/hg/lib/bamFile.c	14 Sep 2009 23:44:25 -0000	1.7
@@ -1,267 +1,279 @@
 /* bam -- interface to binary alignment format files using Heng Li's samtools lib. */
 
 #ifdef USE_BAM
 
 #include "common.h"
 #include "hdb.h"
 #include "bamFile.h"
 
 static char const rcsid[] = "$Id$";
 
 static boolean ignoreStrand = FALSE;
 
 void bamIgnoreStrand()
 /* Change the behavior of this lib to disregard item strand. 
  * If called, this should be called before any other bam functions. */
 {
 ignoreStrand = TRUE;
 }
 
-static char *bbiNameFromTable(struct sqlConnection *conn, char *table)
-/* Return file name from little table. */
-/* This should be libified somewhere sensible -- copied from hgTracks/bedTrack.c. */
+char *bamFileNameFromTable(char *db, char *table, char *bamSeqName)
+/* Return file name from table.  If table has a seqName column, then grab the 
+ * row associated with bamSeqName (which is not nec. in chromInfo, e.g. 
+ * bam file might have '1' not 'chr1'). */
 {
-char query[256];
-safef(query, sizeof(query), "select fileName from %s", table);
+struct sqlConnection *conn = hAllocConn(db);
+boolean checkSeqName = (sqlFieldIndex(conn, table, "seqName") >= 0);
+if (checkSeqName && bamSeqName == NULL)
+    errAbort("bamFileNameFromTable: table %s has seqName column, but NULL seqName passed in",
+	     table);
+char query[512];
+if (checkSeqName)
+    safef(query, sizeof(query), "select fileName from %s where seqName = '%s'",
+	  table, bamSeqName);
+else
+    safef(query, sizeof(query), "select fileName from %s", table);
 char *fileName = sqlQuickString(conn, query);
 if (fileName == NULL)
+    {
+    if (checkSeqName)
+	errAbort("Missing fileName for seqName '%s' in %s table", bamSeqName, table);
+    else
     errAbort("Missing fileName in %s table", table);
+    }
+hFreeConn(&conn);
 return fileName;
 }
 
-void bamFetch(char *db, char *table, char *position, bam_fetch_f callbackFunc, void *callbackData)
-/* Open the .bam file given in db.table, fetch items in the seq:start-end position range,
+void bamFetch(char *bamFileName, char *position, bam_fetch_f callbackFunc, void *callbackData)
+/* 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. 
  * Note: if sequences in .bam file don't begin with "chr" but cart position does, pass in 
  * cart position + strlen("chr") to match the .bam file sequence names. */
 {
-// TODO: if bamFile is URL, convert URL to path a la UDC, but under udcFuse mountpoint.
-// new hg.conf setting for udcFuse mountpoint/support.
-struct sqlConnection *conn = hAllocConn(db);
-char *bamFileName = bbiNameFromTable(conn, table);
-hFreeConn(&conn);
-
 samfile_t *fh = samopen(bamFileName, "rb", NULL);
 if (fh == NULL)
     errAbort("samopen(%s, \"rb\") returned NULL", bamFileName);
 
 int chromId, start, end;
 int ret = bam_parse_region(fh->header, position, &chromId, &start, &end);
 if (ret != 0)
     errAbort("bam_parse_region(%s) failed (%d)", position, ret);
 //?? Could this happen if there is no data on some _random?  can avoid with tdb chromosomes...
 
 bam_index_t *idx = bam_index_load(bamFileName);
+if (idx == NULL)
+    errAbort("bam_index_load(%s) failed.", bamFileName);
 ret = bam_fetch(fh->x.bam, idx, chromId, start, end, callbackData, callbackFunc);
 if (ret != 0)
     errAbort("bam_fetch(%s, %s (chromId=%d) failed (%d)", bamFileName, position, chromId, ret);
 samclose(fh);
 }
 
 boolean bamIsRc(const bam1_t *bam)
 /* Return TRUE if alignment is on - strand.  If bamIgnoreStrand has been called,
  * then this always returns FALSE. */
 {
 const bam1_core_t *core = &bam->core;
 return (core->flag & BAM_FREVERSE) && !ignoreStrand;
 }
 
 char *bamGetQuerySequence(const bam1_t *bam)
 /* Return the nucleotide sequence encoded in bam.  The BAM format 
  * reverse-complements query sequence when the alignment is on the - strand,
  * so here we rev-comp it back to restore the original query sequence. */
 {
 const bam1_core_t *core = &bam->core;
 char *qSeq = needMem(core->l_qseq + 1);
 uint8_t *s = bam1_seq(bam);
 int i;
 for (i = 0; i < core->l_qseq; i++)
     qSeq[i] = bam_nt16_rev_table[bam1_seqi(s, i)];
 if (bamIsRc(bam))
     reverseComplement(qSeq, core->l_qseq);
 return qSeq;
 }
 
 char *bamGetCigar(const bam1_t *bam)
 /* Return a BAM-enhanced CIGAR string, decoded from the packed encoding in bam. */
 {
 unsigned int *cigarPacked = bam1_cigar(bam);
 const bam1_core_t *core = &bam->core;
 struct dyString *dyCigar = dyStringNew(min(8, core->n_cigar*4));
 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);
     }
 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);
 	}
     }
 }
 
 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
 	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	    break;
 	case 'D': // deleted from query
 	case 'N': // long deletion from query (intron as opposed to small del)
 	    tLength += n;
 	    break;
 	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;
 }
 
 struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset)
 /* Convert from bam to ffAli format.  (Adapted from psl.c's pslToFfAli.) */
 {
 struct ffAli *ffList = NULL, *ff;
 const bam1_core_t *core = &bam->core;
 boolean isRc = bamIsRc(bam);
 DNA *needle = (DNA *)bamGetQuerySequence(bam);
 if (isRc)
     reverseComplement(target->dna, target->size);
 DNA *haystack = target->dna;
 unsigned int *cigarPacked = bam1_cigar(bam);
 int tStart = targetOffset, qStart = 0, i;
 // If isRc, need to go through the CIGAR ops backwards, but sequence offsets still count up.
 int iStart = isRc ? (core->n_cigar - 1) : 0;
 int iIncr = isRc ? -1 : 1;
 for (i = iStart;  isRc ? (i >= 0) : (i < core->n_cigar);  i += iIncr)
     {
     char op;
     int size = bamUnpackCigarElement(cigarPacked[i], &op);
     switch (op)
 	{
 	case 'M': // match or mismatch (gapless aligned block)
 	    AllocVar(ff);
 	    ff->left = ffList;
 	    ffList = ff;
 	    ff->nStart = needle + qStart;
 	    ff->nEnd = ff->nStart + size;
 	    ff->hStart = haystack + tStart - targetOffset;
 	    ff->hEnd = ff->hStart + size;
 	    tStart += size;
 	    qStart += size;
 	    break;
 	case 'I': // inserted in query
 	case 'S': // skipped query bases at beginning or end ("soft clipping")
 	    qStart += size;
 	    break;
 	case 'D': // deleted from query
 	case 'N': // long deletion from query (intron as opposed to small del)
 	    tStart += size;
 	    break;
 	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("bamToFfAli: unrecognized CIGAR op %c -- update me", op);
 	}
     }
 ffList = ffMakeRightLinks(ffList);
 ffCountGoodEnds(ffList);
 return ffList;
 }
 
 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')
 	{
 	while (*s) putc(*s++, stdout);
 	++s;
 	}
     }
 putc('\n', stdout);
 }
 
 #endif//def USE_BAM