struct slName *randomBamIds(char *table, struct sqlConnection *conn, int count)
/* Return some semi-random qName based IDs from a BAM file. */
{
/* Read 10000 items from bam file, or if they ask for a big list, then 4x what they ask for. */
char *fileName = bamFileName(table, conn, NULL);
samfile_t *fh = bamOpen(fileName, NULL);
struct lm *lm = lmInit(0);
int orderedCount = count * 4;
if (orderedCount < 10000)
orderedCount = 10000;
struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, orderedCount, lm);
/* Shuffle list and extract qNames from first count of them. */
shuffleList(&samList);
struct slName *randomIdList = NULL;
int i;
for (i=0, sam = samList; i<count && sam != NULL; ++i, sam = sam->next)
slNameAddHead(&randomIdList, sam->qName);
/* Clean up and go home. */
lmCleanup(&lm);
bamClose(&fh);
freez(&fileName);
return randomIdList;
}
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. */
{
char *bamFileName = NULL;
samfile_t *fh = bamOpen(fileOrUrl, &bamFileName);
boolean usingUrl = TRUE;
usingUrl = (strstr(fileOrUrl, "tp://") || strstr(fileOrUrl, "https://"));
if (pSamFile != NULL)
*pSamFile = fh;
#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
{
bamFetchAlreadyOpen(fh, idx, bamFileName, position, callbackFunc, callbackData);
free(idx); // Not freeMem, freez etc -- sam just uses malloc/calloc.
}
bamClose(&fh);
}
void showSchemaBam(char *table, struct trackDb *tdb)
/* Show schema on bam. */
{
struct sqlConnection *conn = NULL;
if (!trackHubDatabase(database))
conn = hAllocConn(database);
char *fileName = bamFileName(table, conn, NULL);
struct asObject *as = bamAsObj();
hPrintf("<B>Database:</B> %s", database);
hPrintf(" <B>Primary Table:</B> %s<br>", table);
hPrintf("<B>BAM File:</B> %s", fileName);
hPrintf("<BR>\n");
hPrintf("<B>Format description:</B> %s<BR>", as->comment);
hPrintf("See the <A HREF=\"%s\" target=_blank>SAM Format Specification</A> for more details<BR>\n",
"http://samtools.sourceforge.net/SAM1.pdf");
/* Put up table that describes fields. */
hTableStart();
hPrintf("<TR><TH>field</TH>");
hPrintf("<TH>description</TH> ");
puts("</TR>\n");
struct asColumn *col;
int colCount = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TR><TD><TT>%s</TT></TD>", col->name);
hPrintf("<TD>%s</TD></TR>", col->comment);
++colCount;
}
hTableEnd();
/* Put up another section with sample rows. */
webNewSection("Sample Rows");
hTableStart();
/* Print field names as column headers for example */
hPrintf("<TR>");
int colIx = 0;
for (col = as->columnList; col != NULL; col = col->next)
{
hPrintf("<TH>%s</TH>", col->name);
++colIx;
}
hPrintf("</TR>\n");
/* Fetch sample rows. */
samfile_t *fh = bamOpen(fileName, NULL);
struct lm *lm = lmInit(0);
struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm);
/* Print sample lines. */
char *row[SAMALIGNMENT_NUM_COLS];
char numBuf[BAM_NUM_BUF_SIZE];
for (sam=samList; sam != NULL; sam = sam->next)
{
samAlignmentToRow(sam, numBuf, row);
hPrintf("<TR>");
for (colIx=0; colIx<colCount; ++colIx)
{
hPrintf("<TD>");
xmlEscapeStringToFile(row[colIx], stdout);
hPrintf("</TD>");
}
hPrintf("</TR>\n");
}
hTableEnd();
printTrackHtml(tdb);
/* Clean up and go home. */
bamClose(&fh);
lmCleanup(&lm);
freeMem(fileName);
hFreeConn(&conn);
}
