src/inc/bwgInternal.h

@@ -112,7 +112,7 @@ struct bbiSummary *bwgReduceSectionList(struct bwgSection *sectionList,
 
 void bwgCreate(struct bwgSection *sectionList, struct hash *chromSizeHash, 
 	int blockSize, int itemsPerSlot, boolean doCompress, boolean keepAllChromosomes,
-        boolean fixedSummaries, char *fileName);
+        boolean fixedSummaries, boolean clipDontDie, char *fileName);
 /* Create a bigWig file out of a sorted sectionList.  A lower level routine
  * than the one above. */
 

src/inc/common.mk

@@ -81,7 +81,7 @@ ifneq (${SSL_DIR}, "/usr/include/openssl")
 endif
 # on hgwdev, already using the static library with mysqllient.
 ifeq (${IS_HGWDEV},yes)
-   L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5
+   L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl
 else
    L+=-lssl -lcrypto
 endif
@@ -89,7 +89,7 @@ endif
 # autodetect where libm is installed
 ifeq (${MLIB},)
   ifneq ($(wildcard /usr/lib64/libm.a),)
-      MLIB=/usr/lib64/libm.a
+      MLIB=-lm
   endif
 endif
 ifeq (${MLIB},)
@@ -138,7 +138,7 @@ ifneq ($(MAKECMDGOALS),clean)
   # on hgwdev, use the static library.
   ifeq (${IS_HGWDEV},yes)
     MYSQLINC=/usr/include/mysql
-    MYSQLLIBS=/usr/lib64/libssl.a /usr/lib64/libcrypto.a /usr/lib64/mysql/libmysqlclient.a -lkrb5
+    MYSQLLIBS=/usr/lib64/libmysqlclient.a /usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -ldl -lz
   endif
   # this does *not* work on Mac OSX with the dynamic libraries
   ifneq ($(UNAME_S),Darwin)
@@ -239,7 +239,7 @@ endif
 # OK to add -lstdc++ to all MYSQLLIBS just in case it is
 #    MySQL version 5.6 libraries, but no 'librt' on Mac OSX
 ifeq (${IS_HGWDEV},yes)
-  MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.a /usr/lib/debug/usr/lib64/librt.a
+  MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.8.5/libstdc++.a /usr/lib64/librt.a
 else
   ifeq ($(UNAME_S),Darwin)
     MYSQLLIBS += -lstdc++
@@ -261,7 +261,7 @@ endif
 #global external libraries
 L += $(kentSrc)/htslib/libhts.a
 
-L+=${PNGLIB} ${ZLIB} ${MLIB}
+L+=${PNGLIB} ${MLIB} ${ZLIB}
 HG_INC+=${PNGINCL}
 
 # pass through COREDUMP

src/inc/gff3.h

@@ -6,6 +6,7 @@
 #ifndef gff3_h
 #define gff3_h
 
+
 struct gff3Ann
 /* Annotation record from a GFF3 file.  Attributes define in the spec (those
  * starting with upper case letters) are parsed into fields of this
@@ -140,6 +141,10 @@ struct gff3Ann
                              * if not known */
 };
 
+/* flags */
+#define GFF3_WARN_WHEN_POSSIBLE 0x01  // generate warnings and drop entries rather than errors
+
+
 struct gff3AnnRef
 /* A reference to a gff3Ann object */
 {
@@ -191,6 +196,7 @@ struct gff3File
                                           * NULL if none specified */
     struct lineFile *lf;                 /* only set while parsing */
     FILE *errFh;            /* write errors to this file */
+    unsigned int flags;     /* flags controlling parsing */
     int maxErr;             /* maximum number of errors before aborting */
     int errCnt;             /* error count */
 };
@@ -229,11 +235,11 @@ extern char *gff3FeatJGeneSegment;
 extern char *gff3FeatVGeneSegment;
 
 
-struct gff3File *gff3FileOpen(char *fileName, int maxErr, FILE *errFh);
+struct gff3File *gff3FileOpen(char *fileName, int maxErr, unsigned flags, FILE *errFh);
 /* Parse a GFF3 file into a gff3File object.  If maxErr not zero, then
  * continue to parse until this number of error have been reached.  A maxErr
  * less than zero does not stop reports all errors. Write errors to errFh,
- * if NULL, use stderr. */
+ * if NULL, use stderr.  See above flags. */
 
 void gff3FileFree(struct gff3File **g3fPtr);
 /* Free a gff3File object */

src/inc/jointalign.h

 /*****************************************************************************
  * Copyright (C) 2002 Ryan Weber.  This source code may be freely used       *
  * for personal, academic, and non-profit purposes.  Commercial use          *
- * permitted only by explicit agreement with Ryan Weber (weber@cse.ucsc.edu) *
+ * permitted only by explicit agreement with Ryan Weber (weber@soe.ucsc.edu) *
  *****************************************************************************/
 /* jointalign.h - routines for printing a joint alignment in html. */
 

src/inc/srcVersion.h

 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
-#define SRC_VERSION "365"
+#define SRC_VERSION "370"

src/inc/vcf.h

@@ -176,6 +176,9 @@ switch (type)
 	fprintf(f, "%c", datum.datChar);
 	break;
     case vcfInfoString:
+        if (startsWith("http", datum.datString))
+            fprintf(f, "<a target=_blank href='%s'>%s</a>", datum.datString, datum.datString);
+        else
             fprintf(f, "%s", datum.datString);
 	break;
     default:

src/lib/bwgCreate.c

@@ -361,6 +361,27 @@ for (item = itemList; item != NULL; )
 lmCleanup(&lmLocal);
 }
 
+static bits32 getChromSize(struct hash *chromSizeHash, char *chrom, boolean clipDontDie)
+/* return size of chrom or BIGNUM if hash is NULL. errAbort if not found, unless clipDontDie */
+{
+int chromSize = 0;
+if (chromSizeHash) {
+    chromSize = hashIntValDefault(chromSizeHash, chrom, -1);
+    if (chromSize==-1) {
+        warn("chromosome %s is not in chrom sizes file", chrom);
+
+        if (clipDontDie)
+            chromSize = BIGNUM;
+        else
+            noWarnAbort();
+    }
+}
+else
+    chromSize = BIGNUM;
+
+return chromSize;
+}
+
 static unsigned parseUnsignedVal(struct lineFile *lf, char *var, char *val)
 /* Return val as an integer, printing error message if it's not. */
 {
@@ -420,7 +441,9 @@ while ((varEqVal = nextWord(&initialLine)) != NULL)
  * rest of section. */
 if (chrom == NULL)
     errAbort("Missing chrom= setting line %d of %s\n", lf->lineIx, lf->fileName);
-bits32 chromSize = (chromSizeHash ? hashIntVal(chromSizeHash, chrom) : BIGNUM);
+
+bits32 chromSize = getChromSize(chromSizeHash, chrom, clipDontDie);
+
 if (start > chromSize)
     {
     warn("line %d of %s: chromosome %s has %u bases, but item starts at %u",
@@ -502,7 +525,7 @@ while (lineFileNextReal(lf, &line))
         {
 	lmAllocVar(chromHash->lm, chrom);
 	hashAddSaveName(chromHash, chromName, chrom, &chrom->name);
-	chrom->size = (chromSizeHash ? hashIntVal(chromSizeHash, chromName) : BIGNUM);
+	chrom->size = getChromSize(chromSizeHash, chromName, clipDontDie);
 	slAddHead(&chromList, chrom);
 	}
 
@@ -585,7 +608,7 @@ chromList = NULL;
 }
 
 void bwgMakeChromInfo(struct bwgSection *sectionList, struct hash *chromSizeHash,
-	int *retChromCount, struct bbiChromInfo **retChromArray,
+	boolean clipDontDie, int *retChromCount, struct bbiChromInfo **retChromArray,
 	int *retMaxChromNameSize)
 /* Fill in chromId field in sectionList.  Return array of chromosome name/ids. 
  * The chromSizeHash is keyed by name, and has int values. */
@@ -619,7 +642,7 @@ for (i = 0, uniq = uniqList; i < chromCount; ++i, uniq = uniq->next)
     {
     chromArray[i].name = uniq->val;
     chromArray[i].id = i;
-    chromArray[i].size = hashIntVal(chromSizeHash, uniq->val);
+    chromArray[i].size = getChromSize(chromSizeHash, uniq->val, clipDontDie);
     }
 
 /* Clean up, set return values and go home. */
@@ -636,7 +659,7 @@ static int bwgStrcmp (const void * A, const void * B) {
 }
 
 void bwgMakeAllChromInfo(struct bwgSection *sectionList, struct hash *chromSizeHash,
-	int *retChromCount, struct bbiChromInfo **retChromArray,
+	boolean clipDontDie, int *retChromCount, struct bbiChromInfo **retChromArray,
 	int *retMaxChromNameSize)
 /* Fill in chromId field in sectionList.  Return array of chromosome name/ids. 
  * The chromSizeHash is keyed by name, and has int values. */
@@ -667,7 +690,7 @@ for (i = 0; i < chromCount; ++i)
     {
     chromArray[i].name = chromNames[i];
     chromArray[i].id = i;
-    chromArray[i].size = hashIntVal(chromSizeHash, chromNames[i]);
+    chromArray[i].size = getChromSize(chromSizeHash, chromNames[i], clipDontDie);
     }
 
 // Assign IDs to sections:
@@ -956,7 +979,7 @@ for (i=1; i<REDUCTION_COUNT; i++)
 
 void bwgCreate(struct bwgSection *sectionList, struct hash *chromSizeHash, 
 	int blockSize, int itemsPerSlot, boolean doCompress, boolean keepAllChromosomes,
-        boolean fixedSummaries, char *fileName)
+        boolean fixedSummaries, boolean clipDontDie, char *fileName)
 /* Create a bigWig file out of a sorted sectionList. */
 {
 bits64 sectionCount = slCount(sectionList);
@@ -984,9 +1007,9 @@ int i;
 struct bbiChromInfo *chromInfoArray;
 int chromCount, maxChromNameSize;
 if (keepAllChromosomes)
-    bwgMakeAllChromInfo(sectionList, chromSizeHash, &chromCount, &chromInfoArray, &maxChromNameSize);
+    bwgMakeAllChromInfo(sectionList, chromSizeHash, clipDontDie, &chromCount, &chromInfoArray, &maxChromNameSize);
 else
-    bwgMakeChromInfo(sectionList, chromSizeHash, &chromCount, &chromInfoArray, &maxChromNameSize);
+    bwgMakeChromInfo(sectionList, chromSizeHash, clipDontDie, &chromCount, &chromInfoArray, &maxChromNameSize);
 
 if (fixedSummaries) 
     bwgComputeFixedSummaries(sectionList, reduceSummaries, &summaryCount, chromInfoArray, reductionAmounts);
@@ -1217,7 +1240,7 @@ struct lm *lm = lmInit(0);
 struct bwgSection *sectionList = bwgParseWig(inName, clipDontDie, chromSizeHash, itemsPerSlot, lm);
 if (sectionList == NULL)
     errAbort("%s is empty of data", inName);
-bwgCreate(sectionList, chromSizeHash, blockSize, itemsPerSlot, compress, keepAllChromosomes, fixedSummaries, outName);
+bwgCreate(sectionList, chromSizeHash, blockSize, itemsPerSlot, compress, keepAllChromosomes, fixedSummaries, clipDontDie, outName);
 lmCleanup(&lm);
 }
 

src/lib/gff3.c

@@ -69,45 +69,51 @@ static bool gff3FileStopDueToErrors(struct gff3File *g3f)
 return g3f->errCnt > g3f->maxErr;
 }
 
-static void gff3FileErr(struct gff3File *g3f, char *format, ...)
+static void gff3FileErr(struct gff3File *g3f, bool canWarn, char *format, ...)
 #if defined(__GNUC__)
-__attribute__((format(printf, 2, 3)))
+__attribute__((format(printf, 3, 4)))
 #endif
 ;
 
-static void gff3AnnErr(struct gff3Ann *g3a, char *format, ...)
+static void gff3AnnErr(struct gff3Ann *g3a, bool canWarn, char *format, ...)
 #if defined(__GNUC__)
-__attribute__((format(printf, 2, 3)))
+__attribute__((format(printf, 3, 4)))
 #endif
 ;
 
-static void vaGff3FileErr(struct gff3File *g3f, char *format, va_list args)
+static void vaGff3FileErr(struct gff3File *g3f, bool canWarn, char *format, va_list args)
 /* Print error message to error file, abort if max errors have been reached */
 {
+bool isWarning = canWarn && (g3f->flags & GFF3_WARN_WHEN_POSSIBLE);
 if (g3f->lf != NULL)
     fprintf(g3f->errFh, "%s:%d: ", g3f->lf->fileName, g3f->lf->lineIx);
+if (isWarning)
+    fprintf(g3f->errFh, "WARNING: ");
 vfprintf(g3f->errFh, format, args);
 fprintf(g3f->errFh, "\n");
+if (!isWarning)
+    {
     g3f->errCnt++;
     if (gff3FileStopDueToErrors(g3f))
         errAbort("GFF3: %d parser errors", g3f->errCnt);
     }
+}
 
-static void gff3FileErr(struct gff3File *g3f, char *format, ...)
+static void gff3FileErr(struct gff3File *g3f, bool canWarn, char *format, ...)
 /* Print error message and abort */
 {
 va_list args;
 va_start(args, format);
-vaGff3FileErr(g3f, format, args);
+vaGff3FileErr(g3f, canWarn, format, args);
 va_end(args);
 }
 
-static void gff3AnnErr(struct gff3Ann *g3a, char *format, ...)
+static void gff3AnnErr(struct gff3Ann *g3a, bool canWarn, char *format, ...)
 /* Print error message abort */
 {
 va_list args;
 va_start(args, format);
-vaGff3FileErr(g3a->file, format, args);
+vaGff3FileErr(g3a->file, canWarn, format, args);
 va_end(args);
 }
 
@@ -117,7 +123,7 @@ static int gff3FileStrToInt(struct gff3File *g3f, char *str)
 char *end;
 long val = strtol(str, &end, 0);
 if ((end == str) || (*end != '\0'))
-    gff3FileErr(g3f, "invalid integer: %s", str);
+    gff3FileErr(g3f, FALSE, "invalid integer: %s", str);
 return (int)val;
 }
 
@@ -127,7 +133,7 @@ static float gff3FileStrToFloat(struct gff3File *g3f, char *str)
 char *end;
 double val = strtod(str, &end);
 if ((end == str) || (*end != '\0'))
-    gff3FileErr(g3f, "invalid float: %s", str);
+    gff3FileErr(g3f, FALSE, "invalid float: %s", str);
 return (float)val;
 }
 
@@ -164,7 +170,7 @@ static char **dynChopStringWhite(struct gff3File *g3f, char *str, int minWords,
 int numWords = chopByWhite(str, NULL, 0);
 if ((numWords < minWords) || (numWords > maxWords))
     {
-    gff3FileErr(g3f, "expected %s, got \"%s\"", desc, str);
+    gff3FileErr(g3f, FALSE, "expected %s, got \"%s\"", desc, str);
     return NULL;
     }
 // allocate buffer for both array and string
@@ -212,7 +218,7 @@ return NULL;
 static void raiseInvalidEscape(struct gff3Ann *g3a, char *str)
 /* raise an error about an invalid escape in a string */
 {
-gff3AnnErr(g3a, "invalid GFF escape sequence in string: %s", str);
+gff3AnnErr(g3a, TRUE, "invalid GFF escape sequence in string: %s", str);
 }
 
 static char convertEscape(struct gff3Ann *g3a, char *esc, char *src)
@@ -220,13 +226,19 @@ static char convertEscape(struct gff3Ann *g3a, char *esc, char *src)
  * in the form `%09' */
 {
 if (!(isxdigit(esc[1]) && isxdigit(esc[2])))
+    {
     raiseInvalidEscape(g3a, src);
+    return '_';  // something
+    }
 char num[3], *end;
 strncpy(num, esc+1, 2);
 num[2] = '\0';
 long val = strtol(num, &end, 16);
 if ((end == num) || (*end != '\0'))
+    {
     raiseInvalidEscape(g3a, src);
+    return '_';
+    }
 return (char)val;
 }
 
@@ -314,7 +326,10 @@ else if (sameString(strand, "-"))
 else if (sameString(strand, "?"))
     return "?";
 else
-    gff3AnnErr(g3a, "invalid strand: '%s'", strand);
+    {
+    gff3AnnErr(g3a, TRUE, "invalid strand: '%s'", strand);
+    return NULL;
+    }
 return NULL;
 }
 
@@ -325,7 +340,10 @@ if (sameString(str, "."))
     return -1;
 int phase = gff3FileStrToInt(g3a->file, str);
 if ((phase < 0) || (phase  > 2))
-    gff3AnnErr(g3a, "invalid phase: %d", phase);
+    {
+    gff3AnnErr(g3a, TRUE, "invalid phase: %d", phase);
+    return -1;
+    }
 return phase;
 }
 
@@ -347,14 +365,14 @@ g3a->phase = parsePhase(g3a, words[7]);
 if (sameString(g3a->type, "CDS"))
     {
     if (g3a->phase < 0)
-	gff3AnnErr(g3a, "CDS feature must have phase");
+	gff3AnnErr(g3a, TRUE, "CDS feature must have phase");
     }
 else
     {
 #if 0 // spec unclear; bug report filed
     // spec currently doesn't restrict phase, unclear if it's allowed on start/stop codon features
     if (g3a->phase >= 0)
-        gff3AnnErr(g3a, "phase only allowed on CDS features");
+        gff3AnnErr(g3a, TRUE, "phase only allowed on CDS features");
 #endif
     }
 }
@@ -364,14 +382,18 @@ static boolean checkAttrTag(struct gff3Ann *g3a, char *tag)
 {
 // FIXME: spec is not clear on what is a valid tag.
 char *tc = tag;
-boolean isOk = isalpha(*tc);
+boolean isOk = (isalnum(*tc) || (*tc == '-') || (*tc == '_'));
 for (tc++; isOk && (*tc != '\0'); tc++)
     {
     if (!((*tc == '-') || (*tc == '_') || isalnum(*tc)))
         isOk = FALSE;
     }
 if (!isOk)
-    gff3AnnErr(g3a, "invalid attribute tag, must start with an alphabetic character and be composed of alphanumeric, dash, or underscore characters: %s", tag);
+    {
+    gff3AnnErr(g3a, TRUE, "invalid attribute tag, must be only alphanumeric, dash or underscore: %s", tag);
+    if (g3a->file->flags & GFF3_WARN_WHEN_POSSIBLE)
+        return TRUE;
+    }
 return isOk;
 }
 
@@ -411,7 +433,7 @@ static void parseAttr(struct gff3Ann *g3a, char *attrStr)
 {
 char *eq = strchr(attrStr, '=');
 if ((eq == NULL) || (eq == attrStr))
-    gff3AnnErr(g3a, "expected name=value: %s", attrStr);
+    gff3AnnErr(g3a, FALSE, "expected name=value: %s", attrStr);
 else
     {
     char *tag = attrStr;
@@ -443,7 +465,7 @@ static void checkSingleValAttr(struct gff3Ann *g3a, struct gff3Attr *attr)
 /* validate that an attribute has only one value */
 {
 if (attr->vals->next != NULL)
-    gff3AnnErr(g3a, "attribute %s must have a single value, found multiple comma-separated values", attr->tag);
+    gff3AnnErr(g3a, FALSE, "attribute %s must have a single value, found multiple comma-separated values", attr->tag);
 }
 
 static void parseIDAttr(struct gff3Ann *g3a, struct gff3Attr *attr)
@@ -564,7 +586,7 @@ else if (sameString(attr->tag, gff3AttrDbxref))
 else if (sameString(attr->tag, gff3AttrOntologyTerm))
     parseOntologyTermAttr(g3a, attr);
 else
-    gff3AnnErr(g3a, "unknown standard attribute, user defined attributes must start with a lower-case letter: %s", attr->tag);
+    gff3AnnErr(g3a, TRUE, "unknown standard attribute, user defined attributes must start with a lower-case letter: %s", attr->tag);
 }
 
 static void parseStdAttrs(struct gff3Ann *g3a)
@@ -587,7 +609,7 @@ static void parseAnn(struct gff3File *g3f, char *line)
 char *words[gffNumCols+1];
 int numWords = chopString(line, "\t", words, gffNumCols+1);
 if (numWords != gffNumCols)
-    gff3FileErr(g3f, "expected %d tab-separated columns: %s", gffNumCols, line);
+    gff3FileErr(g3f, FALSE, "expected %d tab-separated columns: %s", gffNumCols, line);
 else
     {
     struct gff3Ann *g3a = gff3FileAlloc(g3f, sizeof(struct gff3Ann));
@@ -706,7 +728,7 @@ if (g3f->seqRegionMap == NULL)
     g3f->seqRegionMap = hashNew(0);
 struct hashEl *hel = hashStore(g3f->seqRegionMap, sr->seqid);
 if (hel->val != NULL)
-    gff3FileErr(g3f, "duplicate ##sequence-region for %s", sr->seqid);
+    gff3FileErr(g3f, TRUE, "duplicate ##sequence-region for %s", sr->seqid);
 else
     {
     hel->val = sr;
@@ -803,7 +825,10 @@ static void parseGenomeBuild(struct gff3File *g3f, char *line)
 /* parse ##genome-build source buildName */
 {
 if (g3f->genomeBuildSource != NULL)
-    gff3FileErr(g3f, "multiple ##genome-build records");
+    {
+    gff3FileErr(g3f, TRUE, "multiple ##genome-build records");
+    return;  // skip
+    }
 char **words = dynChopStringWhite(g3f, line, 3, 3, NULL,
                                   "\"##genome-build source buildName\"");
 if (words == NULL)
@@ -847,7 +872,7 @@ else if (startsWithWord("##gff-spec-version", line) ||
          startsWithWord("##Type", line))
     ;  /* FIXME: silently ignore these.  Mark says. */
 else
-    gff3FileErr(g3f, "invalid meta line: %s", line);
+    gff3FileErr(g3f, TRUE, "invalid meta line: %s", line);
 }
 
 static void parseLine(struct gff3File *g3f, char *line)
@@ -864,15 +889,15 @@ static void parseHeader(struct gff3File *g3f)
 {
 char *line;
 if (!lineFileNext(g3f->lf, &line, NULL))
-    gff3FileErr(g3f, "empty GFF file, must have header");
+    gff3FileErr(g3f, FALSE, "empty GFF file, must have header");
 char *ver = skipToSpaces(line);
-if (*ver != '\0')
+if ((ver != NULL) && (*ver != '\0'))
     {
     *ver++ = '\0';
     ver = trimSpaces(ver);
     }
 if (!(sameString(line, "##gff-version") && sameString(ver, "3")))
-    gff3FileErr(g3f, "invalid GFF3 header");
+    gff3FileErr(g3f, TRUE, "invalid GFF3 header");
 }
 
 static void parseFile(struct gff3File *g3f)
@@ -907,7 +932,7 @@ struct gff3Ann *g3a2;
 for (g3a2 = g3a->nextPart; (g3a2 != NULL) && !gff3FileStopDueToErrors(g3a->file); g3a2 = g3a2->nextPart)
     {
     if (!sameString(g3a->type, g3a2->type))
-        gff3AnnErr(g3a, "Annotation records for discontinuous features with ID=\"%s\" do not have the same type, found \"%s\" and \"%s\"", g3a->id, g3a->type, g3a2->type);
+        gff3AnnErr(g3a, FALSE, "Annotation records for discontinuous features with ID=\"%s\" do not have the same type, found \"%s\" and \"%s\"", g3a->id, g3a->type, g3a2->type);
     }
 }
 
@@ -978,7 +1003,7 @@ static struct gff3Ann *resolveRef(struct gff3Ann *g3a, char *id, char *attr)
 {
 struct gff3Ann *ann = gff3FileFindAnn(g3a->file, id);
 if (ann == NULL)
-    gff3AnnErr(g3a, "Can't find annotation record \"%s\" referenced by \"%s\" %s attribute", id, g3a->id, attr);
+    gff3AnnErr(g3a, TRUE, "Can't find annotation record \"%s\" referenced by \"%s\" %s attribute", id, g3a->id, attr);
 return ann;
 }
 
@@ -1001,7 +1026,11 @@ static void resolveAnn(struct gff3Ann *g3a)
 {
 g3a->parents = resolveRefs(g3a, g3a->parentIds, gff3AttrParent);
 if (g3a->parents == NULL)
+    {
+    // is droppped if there here ignored errors resolving reference
+    if (g3a->parentIds == NULL)
         slSafeAddHead(&g3a->file->roots, gff3AnnRefAlloc(g3a));
+    }
 else
     {
     struct gff3AnnRef *par;
@@ -1045,7 +1074,7 @@ g3f->pool = hashNew(0);
 return g3f;
 }
 
-struct gff3File *gff3FileOpen(char *fileName, int maxErr, FILE *errFh)
+struct gff3File *gff3FileOpen(char *fileName, int maxErr, unsigned flags, FILE *errFh)
 /* Parse a GFF3 file into a gff3File object.  If maxErr not zero, then
  * continue to parse until this number of error have been reached.  A maxErr
  * less than zero does not stop reports all errors. Write errors to errFh,
@@ -1053,6 +1082,7 @@ struct gff3File *gff3FileOpen(char *fileName, int maxErr, FILE *errFh)
 {
 struct gff3File *g3f = gff3FileNew();
 g3f->fileName = gff3FileCloneStr(g3f, fileName);
+g3f->flags = flags;
 g3f->errFh = (errFh != NULL) ? errFh : stderr;
 g3f->maxErr = (maxErr < 0) ? INT_MAX : maxErr;
 parseFile(g3f);

src/lib/htmshell.c

@@ -1010,7 +1010,7 @@ dyStringAppend(policy, " img-src * data:;");
 dyStringAppend(policy, " img-src 'self'");
 // used by hgGene for modbaseimages in hg/hgc/lowelab.c hg/protein/lib/domains.c hg/hgGene/domains.c
 dyStringAppend(policy, " modbase.compbio.ucsf.edu");  
-dyStringAppend(policy, " hgwdev.cse.ucsc.edu"); // used by visiGene
+dyStringAppend(policy, " hgwdev.gi.ucsc.edu"); // used by visiGene
 dyStringAppend(policy, " genome.ucsc.edu"); // used by visiGene
 dyStringAppend(policy, " code.jquery.com");          // used by hgIntegrator
 dyStringAppend(policy, " www.google-analytics.com"); // used by google analytics

src/lib/net.c

@@ -1625,8 +1625,6 @@ while (TRUE)
 	return TRUE;
 	}
     close(sd);
-    if (redirectCount > 0)
-	freeMem(url);
     if (success)
 	{
 	/* we have a new url to try */
@@ -1653,6 +1651,8 @@ while (TRUE)
 		}
 	    }
 	}
+    if (redirectCount > 1)
+	freeMem(url);
     if (!success)
 	{  /* failure after 0 to 5 redirects */
 	if (redirectCount > 0)

src/lib/psl.c

@@ -1951,7 +1951,7 @@ if (cigar == NULL)
     }
 else
     {
-    char cigarSpec[strlen(cigar+1)];  // copy since parsing is destructive
+    char cigarSpec[strlen(cigar)+1];  // copy since parsing is destructive
     strcpy(cigarSpec, cigar);
     char *cigarNext = cigarSpec;
     if (strand[1] == '-')

src/lib/tagToSql.c

@@ -196,7 +196,7 @@ for (tti = ttiList; tti != NULL; tti = tti->next)
     char *sqlType = NULL;
     char sqlTypeBuf[256];
     if (!isSymbolString(tti->name))
-        errAbort("Error - database needs work. Somehow symbol %s got in field list\n", tti->name);
+        errAbort("Error - tagStorm not SQL compliant. Somehow symbol %s got in field list\n", tti->name);
     if (sqlReservedCheck(reservedHash, tti->name))
         errAbort("Error - field '%s' is a SQL reserved word", tti->name);
     if (tti->isUnsigned)

src/lib/tests/fetchUrlTest.c

@@ -53,6 +53,7 @@ if (startsWith("http://",url) || startsWith("https://",url))
 	/*  Update sd with newSd, replace it with newUrl, etc. */
 	sd = newSd;
 	url = newUrl;
+	verbose(2, "New url after redirect: %s\n", url);
 	}
     }
 while (TRUE)

src/lib/tests/gff3Tester.c

@@ -18,7 +18,7 @@ errAbort(
 static void gff3Tester(char *gff3InFile, char *gff3OutFile)
 /* tester for GFF3 objects */
 {
-struct gff3File *g3f = gff3FileOpen(gff3InFile, -1, NULL);
+struct gff3File *g3f = gff3FileOpen(gff3InFile, -1, 0, NULL);
 gff3FileWrite(g3f, gff3OutFile);
 gff3FileFree(&g3f);
 }

src/lib/tests/htmlMimeTest.c

@@ -17,7 +17,7 @@ errAbort(
 "htmlMimeTest - post mime-encoded page with series on input sizes\n"
 "usage:\n"
 "   htmlMimeTest url-to-hgBlat dnaText startSize endSize\n"
-"e.g. htmlMimeTest http://hgwdev-${user}.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 100 200\n"
+"e.g. htmlMimeTest https://hgwdev-${user}.gi.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 100 200\n"
 "options:\n"
 "   -asFile - send data as type FILE upload (seqFile) instead of TEXTAREA (userSeq) \n"
 );
@@ -35,7 +35,6 @@ void htmlMimeTest(char *url, char *dnaFileName, int size)
 struct htmlPage *rootPage, *page;
 struct htmlForm *form, *mainForm;
 struct qaStatus *qs;
-struct htmlFormVar *orgVar;
 char *dna, *dnaSeg;
 qs = qaPageGet(url, &rootPage);
 if (qs->errMessage)

src/lib/tests/makefile

@@ -168,7 +168,7 @@ ${BIN_DIR}/htmlMimeTest:  mkdirs htmlMimeTest.o ${MYLIBS}
 	${CC} ${COPT} -o ${BIN_DIR}/htmlMimeTest htmlMimeTest.o ${MYLIBS} ${L}
 
 htmlMime1: ${BIN_DIR}/htmlMimeTest mkdirs
-	${BIN_DIR}/htmlMimeTest http://hgwdev.cse.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out
+	${BIN_DIR}/htmlMimeTest https://hgwdev.gi.ucsc.edu/cgi-bin/hgBlat input/htmlMime.txt 3490 3502 > output/$@.out
 	diff expected/$@.out output/$@.out
 
 

src/lib/tests/udcTest.c

@@ -33,7 +33,6 @@ int size = 0;
 // Local copy (reference file) and URL for testing:
 #define THOUSAND_HIVE "/hive/data/outside/1000genomes/ncbi/ftp-trace.ncbi.nih.gov/1000genomes/"
 #define THOUSAND_FTP "ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/"
-#define CHR3_SLX_BAM "NA12878/alignment/NA12878.chrom3.SLX.maq.SRP000032.2009_07.bam"
 #define CHR4_SLX_BAM "NA12878/alignment/NA12878.chrom4.SLX.maq.SRP000032.2009_07.bam"
 
 // Use typical size range of bgzip-compressed data blocks:
@@ -452,7 +451,7 @@ else
 
 if (sameString(protocol, "http"))
     {
-    char *httpUrl = "http://hgwdev.cse.ucsc.edu/~angie/wgEncodeCshlRnaSeqAlignmentsK562ChromatinShort.bb";
+    char *httpUrl = "http://hgwdev.gi.ucsc.edu/~angie/wgEncodeCshlRnaSeqAlignmentsK562ChromatinShort.bb";
     char *httpLocalCopy = "/gbdb/hg18/bbi/wgEncodeCshlRnaSeqAlignmentsK562ChromatinShort.bb";
     if (size)
 	gotError |= testSize(httpUrl, fileSize(httpLocalCopy));

src/utils/bamSplitByChrom/bamSplitByChrom.c

@@ -29,7 +29,7 @@ static struct optionSpec options[] = {
    {NULL, 0},
 };
 
-void closeOutput(struct hash *hash, bam_header_t *head)
+void closeOutput(struct hash *hash)
 /* Loops through the output files and closes them. */
 {
 struct hashEl *hel, *helList = hashElListHash(hash);
@@ -44,7 +44,6 @@ void writeOutput(samfile_t *input,  struct hash *hash, boolean unmapped, char *d
 /* Reads through the input bam and writes each alignment to the correct output file.
  * Unmapped reads are written to 'unmapped.bam' */ 
 {
-bam_header_t *head = input ->header;
 bam1_t one;
 ZeroVar(&one);
 if (makeDir(dir))
@@ -52,6 +51,7 @@ if (makeDir(dir))
     setCurrentDir(dir);
     }
 // Creates a new directory and moves into it. 
+bam_header_t *head = sam_hdr_read(input);
 samfile_t *unmap = bamMustOpenLocal("unmapped.bam", "wb", head);
 if (!unmapped)
     /* Removes the 'unmapped.bam' file if it is not requested. */
@@ -60,11 +60,11 @@ if (!unmapped)
     }
 for (;;)
     {
-    if (samread (input, &one) < 0)
+    if (sam_read1(input, head, &one) < 0)
         {
 	break;
 	}
-    if (one.core.tid > 0)
+    if (one.core.tid >= 0)
 	{
 	char *chrom = head->target_name[one.core.tid];
 	samfile_t *out = hashFindVal(hash, chrom);
@@ -74,13 +74,13 @@ for (;;)
 	    out = bamMustOpenLocal(fileName, "wb", head);
 	    hashAdd(hash, chrom, out);
 	    }
-	samwrite(hashFindVal(hash, head->target_name[one.core.tid]), &one);    
+	sam_write1(hashFindVal(hash, head->target_name[one.core.tid]), head, &one);    
 	}
     else 
 	{
 	if (unmapped)
 	    {
-	    samwrite(unmap, &one);
+	    sam_write1(unmap, head, &one);
 	    }
 	}
     }
@@ -92,11 +92,10 @@ void bamSplitByChrom(char *inBam, char *dir, boolean unmapped)
 {
 struct hash *hash = hashNew(0);
 samfile_t *input = bamMustOpenLocal(inBam, "rb", NULL);
-bam_header_t *head = input ->header;
 writeOutput(input, hash, unmapped, dir);
 /* Open the output bam files in a new directory. */
 /* Write each alignment to the correct output file. */
-closeOutput(hash, head);
+closeOutput(hash);
 /* Loops through each output file and closes it */
 samclose(input);
 }

src/utils/bamSplitByChrom/makefile

+kentSrc = ../..
+kentSrc = ../..
+A = bamSplitByChrom
+include $(kentSrc)/inc/userApp.mk

src/utils/bamToPsl/bamToPsl.c

@@ -114,6 +114,7 @@ for (;;)
               psl->tName = cloneString((char *)hel->val); /* memory leak */
            }
         pslTabOut(psl, f);  /* no free of this psl data, memory leak */
+        pslFree(&psl);
     }
     ++processCount;
     if (dots)