static void validateTag(char *database,struct trackDb *tdb,char *type,char *tag,
boolean firstIsDigitWarning)
// Determines if tag is conforming to rules:
// 1) must exist
// 2) cannot be all numeric.
// 3) Contains only letters, numbers, '_', '-'
// 4) Begins with a letter
// Aborts on 1-3 and optionally warns on 4
{
char *c = tag;
if (*c == '\0')
errAbort("Track %s.%s has no '%s' tag",database,tdb->track,type);
if (!isalpha(*c))
{
if (countLeadingDigits(tag) == strlen(tag))
errAbort("Track %s.%s has all numeric '%s' tag '%s'",database,tdb->track,type,tag);
if (!firstIsDigitWarning)
return;
warn("Track %s.%s has non-conforming '%s' tag '%s' (begins with digit)",
database,tdb->track,type,tag);
}
for (c++;*c != '\0';c++)
{
if (!isalnum(*c) && *c != '_' && *c != '-')
errAbort("Track %s.%s has non-conforming '%s' tag '%s' (contains unsupported characters)",
database,tdb->track,type,tag);
}
}
int cigarWidth(char *cigar, int cigarSize)
/* Return width of alignment as encoded in cigar format string. */
{
int tLength=0;
char *s, *end = cigar + cigarSize;
s = cigar;
while (s < end)
{
int digCount = countLeadingDigits(s);
if (digCount <= 0)
errAbort("expecting number got %s in cigarWidth", s);
int n = atoi(s);
s += digCount;
char op = *s++;
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("cigarWidth: unrecognized CIGAR op %c -- update me", op);
}
}
return tLength;
}
struct dyString *unrepFileName(char *fileName, boolean isSingle)
/* Return string with Rep# in fileName replaced with "Merged" */
{
char *s = strstr(fileName, "Rep");
struct dyString *dy = dyStringNew(0);
if (s == NULL)
{
if (isSingle)
dyStringAppend(dy, fileName);
else
errAbort("No 'Rep' in fileName %s", fileName);
}
else
{
char *pastRep = s + strlen("Rep");
int digitCount = countLeadingDigits(pastRep);
if (digitCount < 1)
errAbort("No digits after 'Rep' in filename %s", fileName);
pastRep += digitCount;
dyStringAppendN(dy, fileName, s-fileName);
dyStringAppend(dy, "Merged");
int len = strlen(pastRep);
if (!isSingle && endsWith(pastRep, ".gz"))
len -= strlen(".gz");
dyStringAppendN(dy, pastRep, len);
}
return dy;
}
INLINE boolean isAllDigits(char *s)
{
return (isNotEmpty(s) && countLeadingDigits(s) == strlen(s));
}
