コード例 #1
0
ファイル: agpGap.c プロジェクト: bowhan/kent
void agpGapFreeList(struct agpGap **pList)
/* Free a list of dynamically allocated agpGap's */
{
struct agpGap *el, *next;

for (el = *pList; el != NULL; el = next)
    {
    next = el->next;
    agpGapFree(&el);
    }
*pList = NULL;
}
コード例 #2
0
ファイル: agpSangerUnfinished.c プロジェクト: bowhan/kent
static void agpSangerUnfinished(char *agpFile, char *contigFasta, char *agpOut)
/* Fix agp to match unfinished contigs in fasta */
{
struct lineFile *lf = lineFileOpen(agpFile, TRUE);
char *line, *words[16];
int lineSize, wordCount;
unsigned lastPos = 0;
struct agpFrag *agp;
struct agpGap *gap;
FILE *f;
char *lastObj = NULL;
f = mustOpen(agpOut, "w");
char *newChrom = NULL;
struct hash *hash = hashFasta(contigFasta);

verbose(2,"#\tprocessing AGP file: %s\n", agpFile);
while (lineFileNext(lf, &line, &lineSize))
    {
    if (line[0] == 0 || line[0] == '#' || line[0] == '\n')
        continue;
    //verbose(2,"#\tline: %d\n", lf->lineIx);
    wordCount = chopLine(line, words);
    if (wordCount < 5)
        errAbort("Bad line %d of %s: need at least 5 words, got %d\n",
		 lf->lineIx, lf->fileName, wordCount);

    if (!lastObj || !sameString(words[0],lastObj))
	{
	freez(&newChrom);
	newChrom = cloneString(words[0]);
	lastPos = 0;
	}

    	
		 
    if (words[4][0] != 'N')
	{
	lineFileExpectAtLeast(lf, 9, wordCount);
	agp = agpFragLoad(words);
	/* agp is 1-based but agp loaders do not adjust for 0-based: */
    	agp->chromStart -= 1;
	agp->fragStart  -= 1;
	if (agp->chromEnd - agp->chromStart != agp->fragEnd - agp->fragStart)
	    errAbort("Sizes don't match in %s and %s line %d of %s\n",
		agp->chrom, agp->frag, lf->lineIx, lf->fileName);

	char *root = cloneString(agp->frag);
	chopSuffixAt(root, '.');

	struct hashEl *e, *elist = hashLookup(hash, root);
	for (e = elist; e; e = hashLookupNext(e))
	    {
	    struct unfinishedContig *u = e->val;
            if ((u->fragStart <= agp->fragStart) && (u->fragEnd >= agp->fragEnd))
		{
		agp->frag = cloneString(u->frag);
		agp->fragEnd -= u->fragStart;
		agp->fragStart -= u->fragStart;
		}
	    }
	freeMem(root);
	}
    else
        {
	lineFileExpectAtLeast(lf, 8, wordCount);
	gap = agpGapLoad(words);
	/* to be consistent with agpFrag */
	gap->chromStart -= 1;
	agp = (struct agpFrag*)gap;
	}

    if (agp->chromStart != lastPos)
	errAbort("Start doesn't match previous end line %d of %s\n"
	    "agp->chromStart: %u\n" 
	    "agp->chromEnd: %u\n" 
	    "lastPos: %u\n" 
	    ,lf->lineIx, lf->fileName
	    ,agp->chromStart
	    ,agp->chromEnd
	    ,lastPos
	    );

    lastPos = agp->chromEnd;
    freez(&lastObj);
    lastObj = cloneString(words[0]); /* not agp->chrom which may be modified already */
	
    if (words[4][0] != 'N')
	{
	/* agpFragOutput assumes 0-based-half-open, but writes 1-based for agp */
	agpFragOutput(agp, f, '\t', '\n');
	agpFragFree(&agp);
	}
    else
        {
	/* restore back to 1-based for agp 
	 * because agpGapOutput doesn't compensate */
	gap->chromStart += 1;
	agpGapOutput(gap, f, '\t', '\n');
	agpGapFree(&gap);
	}
	
    }

carefulClose(&f);
}
コード例 #3
0
static void agpMergeChromScaf(char *agpFile, char *agpOut, boolean filtering)
/* Create a combined agp file from the chrom.agp and scaffold.agp, 
 *  merging in only scaffolds from scaffold.agp
 *  that are not already in chroms. */
{
struct lineFile *lf = lineFileOpen(agpFile, TRUE);
char *line, *words[16];
int lineSize, wordCount;
unsigned lastPos = 0;
struct agpFrag *agp;
struct agpGap *gap;
FILE *f;
char *lastObj = NULL;
f = mustOpen(agpOut, filtering ? "a" : "w");
char *newChrom = NULL;
static struct hash *hash = NULL;
boolean skipping = FALSE;

if (!hash)
    hash = hashNew(0);

verbose(2,"#\tprocessing AGP file: %s\n", agpFile);
while (lineFileNext(lf, &line, &lineSize))
    {
    if (line[0] == 0 || line[0] == '#' || line[0] == '\n')
        continue;
    //verbose(2,"#\tline: %d\n", lf->lineIx);
    wordCount = chopLine(line, words);
    if (wordCount < 5)
        errAbort("Bad line %d of %s: need at least 5 words, got %d\n",
		 lf->lineIx, lf->fileName, wordCount);

    if (!lastObj || !sameString(words[0],lastObj))
	{
	freez(&newChrom);
	newChrom = cloneString(words[0]);
	lastPos = 0;
	}

    	
    skipping = FALSE;
    if (filtering)
	{
	if (hashLookup(hash, words[0]))
	    skipping = TRUE;
	}
		 
    if (words[4][0] != 'N')
	{
	lineFileExpectAtLeast(lf, 9, wordCount);
	agp = agpFragLoad(words);
	/* agp is 1-based but agp loaders do not adjust for 0-based: */
    	agp->chromStart -= 1;
	agp->fragStart  -= 1;
	if (agp->chromEnd - agp->chromStart != agp->fragEnd - agp->fragStart)
	    errAbort("Sizes don't match in %s and %s line %d of %s\n",
		agp->chrom, agp->frag, lf->lineIx, lf->fileName);
        if (!filtering)
	    {
	    char *root = cloneString(agp->frag);
	    chopSuffixAt(root, '.');
	    hashStore(hash, root);
	    freeMem(root);
	    }
	}
    else
        {
	lineFileExpectAtLeast(lf, 8, wordCount);
	gap = agpGapLoad(words);
	/* to be consistent with agpFrag */
	gap->chromStart -= 1;
	agp = (struct agpFrag*)gap;
	}

    if (agp->chromStart != lastPos)
	errAbort("Start doesn't match previous end line %d of %s\n"
	    "agp->chromStart: %u\n" 
	    "agp->chromEnd: %u\n" 
	    "lastPos: %u\n" 
	    ,lf->lineIx, lf->fileName
	    ,agp->chromStart
	    ,agp->chromEnd
	    ,lastPos
	    );

    lastPos = agp->chromEnd;
    freez(&lastObj);
    lastObj = cloneString(words[0]); /* not agp->chrom which may be modified already */
	
    if (words[4][0] != 'N')
	{
	/* agpFragOutput assumes 0-based-half-open, but writes 1-based for agp */
	if (!skipping)
    	    agpFragOutput(agp, f, '\t', '\n');
	agpFragFree(&agp);
	}
    else
        {
	/* restore back to 1-based for agp 
	 * because agpGapOutput doesn't compensate */
	gap->chromStart += 1;
	if (!skipping)
	    agpGapOutput(gap, f, '\t', '\n');
	agpGapFree(&gap);
	}
	
    }

carefulClose(&f);
}