src/hg/gigAssembler/mendMap/mendMap.c 1.11
1.11 2009/07/07 18:45:02 hiram
Fixup broken build on Solaris
Index: src/hg/gigAssembler/mendMap/mendMap.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/gigAssembler/mendMap/mendMap.c,v
retrieving revision 1.10
retrieving revision 1.11
diff -b -B -U 4 -r1.10 -r1.11
--- src/hg/gigAssembler/mendMap/mendMap.c 5 Sep 2003 21:30:43 -0000 1.10
+++ src/hg/gigAssembler/mendMap/mendMap.c 7 Jul 2009 18:45:02 -0000 1.11
@@ -185,9 +185,8 @@
int maxMapDif(struct mmClone *a, struct mmClone *b)
/* Return max distance between clones in map coordinates. */
{
-int fDif, rDif;
int aStart, aEnd, bStart, bEnd;
aStart = a->mapPos;
aEnd = a->mapPos + a->size;
@@ -293,10 +292,8 @@
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[7];
struct mmClone *cloneList = NULL, *clone;
struct hash *cloneHash = newHash(11);
-struct cloneEnd *ce;
-int endCount;
while (lineFileRow(lf, words))
{
if (!sameString(words[3], "0"))
@@ -562,9 +559,8 @@
struct lineFile *lf = lineFileOpen(fileName, TRUE);
char *words[12];
struct overlappingClonePair *ocpList = NULL, *ocp;
struct hash *ocpHash = newHash(12);
-int score;
while (lineFileRow(lf, words))
{
AllocVar(ocp);
@@ -991,10 +987,8 @@
struct dlNode *n1, *n2;
struct dlNode *innerStart, *outerEnd;
struct cloneEnd *ce;
struct mmClone *clone;
-struct overlappingClonePair *ocp;
-char how;
struct fitAt *fit;
int score, minScore;
int missingOverlap, presentOverlap;
int overlapCloneCount = 0;
@@ -1187,9 +1181,8 @@
struct mmClone *clone, boolean ignoreEnds)
/* Return orientation of clone relative to other clone in pair based on end matches.
* Returns 1 (orientForward) if it appears clone comes after other clone. */
{
-int orientation = orientUnknown;
char how, howFlip;
how = ocpHitsHow(ocp, clone, -1, ignoreEnds);
howFlip = ocpHitsHow(ocp, clone, 1, ignoreEnds);
@@ -1220,16 +1213,15 @@
struct hash *ocpHash, boolean ignoreEnds)
/* Return scored list of all places newbie could fit overlapping member
* to left in barge. */
{
-char how, howFlip, newHow;
+char how, howFlip;
int newbieOrientation = 0, memberOrientation;
struct dlNode *node, *firstStart, *n1, *n2;
struct cloneEnd *ce;
struct mmClone *clone;
struct overlappingClonePair *ocp;
struct fitAt *fitList = NULL, *fit;
-int score;
uglyerf("bargeFitListLeft(newbie %s, member %s)\n", newbie->name, member->name);
ce = memStart->val;
memberOrientation = ce->orientation;
@@ -1324,9 +1316,9 @@
struct hash *ocpHash, boolean ignoreEnds)
/* Return scored list of all places newbie could fit overlapping member
* to right in barge. */
{
-char how, howFlip, newHow;
+char how, howFlip;
int newbieOrientation = 0, memberOrientation ;
struct dlNode *node, *lastEnd, *n1, *n2;
struct cloneEnd *ce;
struct mmClone *clone;
@@ -1441,9 +1433,8 @@
/* Attempt to add a clone 'newbie' to barge via connection with 'member'. */
{
struct dlNode *memStart, *memEnd; /* Start/end nodes of member. */
struct overlappingClonePair *ocp;
-int ori;
struct fitAt *leftFits, *rightFits, *fitList, *fit;
logIt("bargeAdd: newbie %s, member %s\n", newbie->name, member->name);
dumpCloneEnds(barge->cloneEndList, logFile);
@@ -1533,9 +1524,8 @@
struct dlNode *n1;
struct cloneEnd *ce;
boolean leftOk, rightOk, addAfter;
struct overlappingClonePair *ocp;
-char *newbieName;
/* Figure out which clone is already part of big barge. */
if (joiningOcp->a->barge == big)
{
@@ -2273,9 +2263,8 @@
struct mmClone *findNextUnenclosed(struct dlNode *node)
/* Find next clone in double-linked clone end list that is
* not enclosed. */
{
-struct mmClone *clone = NULL;
struct cloneEnd *ce;
for (; !dlEnd(node); node = node->next)
{
@@ -2432,13 +2421,9 @@
{
struct cloneRef *aEnd = NULL, *bStart = NULL;
struct bepRef *aBep = NULL, *bBep = NULL, *joiningBep = NULL, *bepRef;
struct bep *bep;
-struct dlNode *node;
int bigEnough = 200000;
-int aEndSize = 0, bStartSize = 0;
-struct mmClone *clone, *lastClone = NULL;
-struct cloneEnd *ce;
boolean bridged = FALSE;
aEnd = getLastClones(aBarge, bigEnough, ocpHash);
bStart = getFirstClones(bBarge, bigEnough, ocpHash);
@@ -2474,16 +2459,8 @@
slFreeList(&bStart);
return bridged;
}
-char *naForNull(char *s)
-/* Return s, or if s is null "n/a" */
-{
-if (s != NULL)
- return s;
-return "n/a";
-}
-
char cloneDir(struct cloneEnd *ce)
/* Return ? + or - for direction clone goes. */
{
int o = ce->orientation;
@@ -2519,9 +2496,9 @@
cloneCount = dlCount(barge->cloneList);
for (eNode = barge->cloneEndList->head; !dlEnd(eNode); eNode = eNode->next)
{
char os, ot, is, it;
- int prevOverlap, nextOverlap;
+ int nextOverlap;
ce = eNode->val;
if (ce->isStart)
{
@@ -2607,16 +2584,12 @@
struct dlNode *bNode, *eNode;
int pos = 0;
struct barge *barge;
struct cloneEnd *ce;
-struct mmClone *clone;
-boolean lastBridged = FALSE;
-
for (bNode = bargeList->head; !dlEnd(bNode); bNode = bNode->next)
{
- struct mmClone *clone, *lastUnenclosed = NULL, *nextUnenclosed;
- struct overlappingClonePair *ocp;
+ struct mmClone *clone, *lastUnenclosed = NULL;
barge = bNode->val;
for (eNode = barge->cloneEndList->head; !dlEnd(eNode); eNode = eNode->next)
{
@@ -2678,8 +2651,9 @@
if (ce->clone == clone && !ce->isStart)
return ce;
}
errAbort("Internal error. Couldn't find end of %s", clone->name);
+return NULL;
}
void setEnclosedPos(struct dlList *bargeList, struct hash *ocpHash, struct hash *bepHash)
/* Set mmPos field of all enclosed clones. */
@@ -2687,9 +2661,8 @@
struct dlNode *bNode, *eNode, *nextEnode = NULL;
int lastPos = 0;
struct barge *barge;
struct cloneEnd *ce, *nextKnownCe, *endCe;
-struct mmClone *clone;
int lastKnownPos, nextKnownPos, knownSpan;
int encCount;
int i;
@@ -2756,9 +2729,9 @@
void orderAndOrientBarges(struct dlList *bargeList, struct hash *ocpHash, struct hash *bepHash)
/* Orient barges according to map and set barge->mapPos field
* according to first clone. */
{
-struct dlNode *bNode, eNode;
+struct dlNode *bNode;
struct barge *barge;
for (bNode = bargeList->head; !dlEnd(bNode); bNode = bNode->next)
{
@@ -2829,9 +2802,9 @@
{
struct cloneEnd *ce;
struct barge *barge = NULL;
struct dlList *bargeList = newDlList();
-int end, lastEnd = -BIGNUM;
+int lastEnd = -BIGNUM;
struct mmClone *clone;
struct dlNode *node;
/* Build up barges literally from map positions. */
@@ -2948,16 +2921,13 @@
{
char fileName[512];
struct mmClone *cloneList = NULL, *clone;
struct hash *cloneHash = NULL;
-struct overlappingClonePair *ocpList = NULL, *ocp;
+struct overlappingClonePair *ocpList = NULL;
struct hash *ocpHash = NULL;
struct dlList *bargeList = NULL;
-struct barge *barge;
-struct dlNode *node;
struct hash *bepHash = NULL;
struct bep *bepList = NULL;
-FILE *f;
/* Set up logging of error and status messages. */
sprintf(fileName, "%s/mmLog.%d", contigDir, version);
logFile = mustOpen(fileName, "w");