debian/changelog

-libucsc (0.0+git20181204.8fcb9fa0+dfsg-1) UNRELEASED; urgency=medium
+libucsc (0.0+git20200121.ba14f430+dfsg-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #xxxxxx)
 
- -- Andreas Tille <tille@debian.org>  Wed, 05 Dec 2018 11:38:35 +0100
+ -- Andreas Tille <tille@debian.org>  Tue, 21 Jan 2020 22:01:46 +0100

debian/compat

-11

debian/control

@@ -3,16 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                libhts-dev,
                libssl-dev,
                libpng-dev,
                libmariadb-java,
                uuid-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/libucsc
 Vcs-Git: https://salsa.debian.org/med-team/libucsc.git
-Homepage: http://genome.ucsc.edu/
+Homepage: https://genome.ucsc.edu/
 
 Package: libucsc0
 Architecture: any

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ucsc
 Upstream-Contact: Jim Kent <jim_kent@pacbell.net>
 Source: git://genome-source.soe.ucsc.edu/kent.git

debian/upstream/metadata

+Bug-Database: https://github.com/ucscGenomeBrowser/kent/issues
+Bug-Submit: https://github.com/ucscGenomeBrowser/kent/issues/new

src/blat/version.doc

@@ -2,6 +2,8 @@
      o (in 36x1) Fixed problem with -fastMap option that made it put in gaps in the
        allignment sometimes when a short mismatch would be a better choice.
      o (in 36x2) Fixed problem with -maxIntron set to non-default value on protein query.
+     o (in 36x3) Added ipv6 support.
+     o (in 36x4) Added _alt support.
 
 36:
      o (in 35x1) added repMatch default values for tileSizes 16 to 18 in genoFind.c

src/blatz/server.c

@@ -20,7 +20,8 @@
 int port = bzpDefaultPort;
 int cpuCount = 2;
 char *host = "localhost";
-unsigned char subnet[4] = {255,255,255,255};
+
+struct cidr *subnet = NULL;
 
 void usage()
 /* Explain usage and exit. */
@@ -38,7 +39,8 @@ printf("Options: (defaults are shown for numerical parameters)\n");
 bzpServerOptionsHelp(bzp);
 bzpClientOptionsHelp(bzp);
 printf("  -debug Writes diagnostic output to console and no daemon fork\n");
-printf("  -subnet=255.255.255.255 Restrict access to subnet\n");
+printf("  -subnet=255.255.255.255 Restrict access to subnet. \n");
+printf("    Supports comma-separated list of IPv4 or IPv6 subnets in CIDR notation, e.g. 255.255.255.255/24\n");
 printf("  -port=%d Use specified TCP/IP port\n", bzpDefaultPort);
 printf("  -host=%s Query specified host\n", host);
 printf("  -cpu=%d Use specified number of CPUs (processes)\n", cpuCount);
@@ -314,7 +316,7 @@ setMaxAlloc(2LL*1024LL*1024LL*1024LL);
 optionInit(&argc, argv, options);
 port = optionInt("port", port);
 host = optionVal("host", host);
-netParseSubnet(optionVal("subnet", NULL), subnet);
+subnet = internetParseSubnetCidr(optionVal("subnet", NULL));
 cpuCount = optionInt("cpu", cpuCount);
 if (argc < 2)
     usage();

src/htslib/knetfile.c

@@ -198,6 +198,11 @@ static SOCKET socket_connect(const char *host, const char *port)
 	server.sin_port = htons(atoi(port));
 	if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
 	// freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
+
+	/* FOR CODE TO CONNECT SUPPORTING IPV6 and IPV4 using our net.c:
+	fd = netConnect(host, port);
+	*/
+
 	return fd;
 }
 #endif

src/htslib/vcf.c

@@ -2099,7 +2099,9 @@ int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
         for (i = 0; i < v->n_info; ++i) {
             bcf_info_t *z = &v->d.info[i];
             if ( !z->vptr ) continue;
-            if ( !first ) kputc(';', s); first = 0;
+            if ( !first )  
+                kputc(';', s); 
+            first = 0; 
             kputs(h->id[BCF_DT_ID][z->key].key, s);
             if (z->len <= 0) continue;
             kputc('=', s);
@@ -2146,7 +2148,9 @@ int vcf_format(const bcf_hdr_t *h, const bcf1_t *v, kstring_t *s)
                 for (i = 0; i < (int)v->n_fmt; ++i) {
                     bcf_fmt_t *f = &fmt[i];
                     if ( !f->p ) continue;
-                    if (!first) kputc(':', s); first = 0;
+                    if (!first) 
+                        kputc(':', s); 
+                    first = 0;
                     if (gt_i == i)
                         bcf_format_gt(f,j,s);
                     else

src/inc/bamFile.h

@@ -50,6 +50,13 @@ samfile_t *bamMustOpenLocal(char *fileName, char *mode, void *extraHeader);
  * The implementation is just a wrapper around samopen from the samtools library
  * that aborts with error message if there's a problem with the open. */
 
+long long bamFileItemCount(char *fileOrUrl, char *baiFileOrUrl);
+/* Return the total number of mapped items across all sequences in fileOrUrl, using index file.
+ * If baiFileOrUrl is NULL, the index file is assumed to be fileOrUrl.bai.
+ * NOTE: not all bam index files include mapped item counts, so this may return 0 even for large
+ * bam.  As of May 2019, our copy of hts_idx_get_stat does not support cram indexes
+ * (perhaps they never include counts?), so this always returns 0 for cram. */
+
 void bamFetchAlreadyOpen(samfile_t *samfile, bam_hdr_t *header,  bam_index_t *idx, char *bamFileName, 
 			 char *position, bam_fetch_f callbackFunc, void *callbackData);
 /* With the open bam file, return items the same way with the callbacks as with bamFetch() */

src/inc/basicBed.h

@@ -321,4 +321,6 @@ boolean asCompareObjAgainstStandardBed(struct asObject *asYours, int numColumnsT
 void loadAndValidateBed(char *row[], int wordCount, int fieldCount, struct lineFile *lf, struct bed * bed, struct asObject *as, boolean isCt);
 /* Convert a row of strings to a bed and validate the contents.  Abort with message if invalid data. Optionally validate bedPlus via asObject. */
 
+int itemRgbColumn(char *column9);
+/* Convert color specification to internal format. */
 #endif /* BASICBED_H */

src/inc/bigBed.h

@@ -143,5 +143,7 @@ struct slName *bigBedListExtraIndexes(struct bbiFile *bbi);
 int bbExtraFieldIndex(struct bbiFile *bbi, char* fieldName);
 /* return the index of a given extra field */
 
+int bbFieldIndex(struct bbiFile *bbi, char* fieldName);
+/* return the index of a given field. Return -1 if not found. */
 #endif /* BIGBED_H */
 

src/inc/bigWig.h

@@ -81,7 +81,7 @@ double bigWigSingleSummary(struct bbiFile *bwf, char *chrom, int start, int end,
     enum bbiSummaryType summaryType, double defaultVal);
 /* Return the summarized single value for a range. */
 
-boolean isBigWig(char *fileName);
+boolean isBigWigFile(char *fileName);
 /* Peak at a file to see if it's bigWig */
 
 boolean bigWigFileCheckSigs(char *fileName);

src/inc/cheapcgi.h

@@ -265,6 +265,12 @@ void cgiEncodeHash(struct hash *hash, struct dyString *dy);
 /* Put a cgi-encoding of a string valued hash into dy.  Tags are always
  * alphabetical to make it easier to compare if two hashes are same. */
 
+void cgiMakeSubmitButtonMaybePressed(char *name, char *value, char *msg, 
+                char *onClick, boolean pressed);
+/* Make 'submit' type button, with optional messsage and onclick javascript, boolean pressed.
+   Set styling to indicate whether button has been pressed (for buttons that change browser mode).
+ */
+
 void cgiMakeButtonWithMsg(char *name, char *value, char *msg);
 /* Make 'submit' type button. Display msg on mouseover, if present*/
 

src/inc/common.h

@@ -176,6 +176,9 @@
 #define uglyAbort errAbort /* debugging error abort. */
 #define uglyOut stdout /* debugging fprintf target. */
 
+unsigned long memCheckPoint();
+/* Return the amount of memory allocated since last called. */
+
 void *needMem(size_t size);
 /* Need mem calls abort if the memory allocation fails. The memory
  * is initialized to zero. */
@@ -979,6 +982,9 @@ int chopByWhiteRespectDoubleQuotes(char *in, char *outArray[], int outSize);
  *   Fred "and Ethyl" results in word [Fred "and Ethyl"]
  * Special note "" is a valid, though empty word. */
 
+int chopByCharRespectDoubleQuotes(char *in, char sep, char *outArray[], int outSize);
+/* Chop a string into sep delimited strings but honor double quotes */
+
 int chopByChar(char *in, char chopper, char *outArray[], int outSize);
 /* Chop based on a single character. */
 
@@ -993,10 +999,10 @@ char *skipBeyondDelimit(char *s,char delimit);
 /* Returns NULL or pointer to first char beyond one (or more contiguous) delimit char.
    If delimit is ' ' then skips beyond first patch of whitespace. */
 
-char *skipLeadingSpaces(char *s);
+char *skipLeadingSpaces(const char *s);
 /* Return first white space or NULL if none.. */
 
-char *skipToSpaces(char *s);
+char *skipToSpaces(const char *s);
 /* Return first white space. */
 
 int eraseTrailingSpaces(char *s);
@@ -1253,12 +1259,12 @@ int intAbs(int a);
 #define roundll(a) ((long long)((a)+0.5))
 /* Round floating point val to nearest long long. */
 
-#ifndef min
+#if !(defined(min) || defined(__cplusplus))
 #define min(a,b) ( (a) < (b) ? (a) : (b) )
 /* Return min of a and b. */
 #endif
 
-#ifndef max
+#if !(defined(max) || defined(__cplusplus))
 #define max(a,b) ( (a) > (b) ? (a) : (b) )
 /* Return max of a and b. */
 #endif

src/inc/common.mk

@@ -43,9 +43,18 @@ ifeq (${PTHREADLIB},)
   PTHREADLIB=-lpthread
 endif
 
+# required extra library on Mac OSX
+ICONVLIB=
+
 # pthreads is required
 ifneq ($(UNAME_S),Darwin)
   L+=${PTHREADLIB}
+else
+  ifneq ($(wildcard /opt/local/lib/libiconv.a),)
+       ICONVLIB=/opt/local/lib/libiconv.a
+  else
+       ICONVLIB=-liconv
+  endif
 endif
 
 # autodetect if openssl is installed
@@ -55,7 +64,7 @@ endif
 
 # autodetect UCSC installation of hal:
 ifeq (${HALDIR},)
-    HALDIR = /hive/groups/browser/hal/halRelease
+    HALDIR = /hive/groups/browser/hal/halRelease/hal.2015-11-11
     ifneq ($(wildcard ${HALDIR}),)
         ifeq (${USE_HAL},)
           USE_HAL=1
@@ -68,6 +77,10 @@ ifeq (${USE_HAL},1)
     HG_DEFS+=-DUSE_HAL
     HG_INC+=-I${HALDIR}/inc
 endif
+# on hgwdev, include HAL by defaults
+ifeq (${IS_HGWDEV},yes)
+   L+=${HALLIBS}
+endif
 
 
 # libssl: disabled by default
@@ -83,7 +96,20 @@ endif
 ifeq (${IS_HGWDEV},yes)
    L+=/usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -lk5crypto -ldl
 else
-   L+=-lssl -lcrypto
+   ifneq ($(wildcard /opt/local/lib/libssl.a),)
+       L+=/opt/local/lib/libssl.a
+   else
+     ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libssl.a),)
+	L+=/usr/lib/x86_64-linux-gnu/libssl.a
+     else
+	L+=-lssl
+     endif
+   endif
+   ifneq ($(wildcard /opt/local/lib/libcrypto.a),)
+       L+=/opt/local/lib/libcrypto.a
+   else
+       L+=-lcrypto
+   endif
 endif
 
 # autodetect where libm is installed
@@ -140,6 +166,11 @@ ifneq ($(MAKECMDGOALS),clean)
     MYSQLINC=/usr/include/mysql
     MYSQLLIBS=/usr/lib64/libmysqlclient.a /usr/lib64/libssl.a /usr/lib64/libcrypto.a -lkrb5 -ldl -lz
   endif
+  ifeq (${MYSQLLIBS},)
+    ifneq ($(wildcard /usr/lib/x86_64-linux-gnu/libmysqlclient.a),)
+	  MYSQLLIBS=/usr/lib/x86_64-linux-gnu/libmysqlclient.a -ldl
+    endif
+  endif
   # this does *not* work on Mac OSX with the dynamic libraries
   ifneq ($(UNAME_S),Darwin)
     ifeq (${MYSQLLIBS},)
@@ -261,7 +292,7 @@ endif
 #global external libraries
 L += $(kentSrc)/htslib/libhts.a
 
-L+=${PNGLIB} ${MLIB} ${ZLIB}
+L+=${PNGLIB} ${MLIB} ${ZLIB} ${ICONVLIB}
 HG_INC+=${PNGINCL}
 
 # pass through COREDUMP

src/inc/dnautil.h

@@ -275,4 +275,8 @@ void aaToAbbr(char aa, char *abbrBuf, size_t abbrBufSize);
 void trimRefAlt(char *ref, char *alt, uint *pStart, uint *pEnd, int *pRefLen, int *pAltLen);
 /* If ref and alt have identical bases at beginning and/or end, trim those & update all params. */
 
+void trimRefAltLeft(char *ref, char *alt, uint *pStart, uint *pEnd, int *pRefLen, int *pAltLen);
+/* If ref and alt have identical bases at beginning and/or end, trim those starting on the right
+ * so we get the leftmost representation & update all params. */
+
 #endif /* DNAUTIL_H */

src/inc/dystring.h

@@ -14,11 +14,11 @@ struct dyString
     {
     struct dyString *next;	/* Next in list. */
     char *string;		/* Current buffer. */
-    int bufSize;		/* Size of buffer. */
-    int stringSize;		/* Size of string. */
+    long bufSize;		/* Size of buffer. */
+    long stringSize;		/* Size of string. */
     };
 
-struct dyString *newDyString(int initialBufSize);
+struct dyString *newDyString(long initialBufSize);
 /* Allocate dynamic string with initial buffer size.  (Pass zero for default) */
 
 #define dyStringNew newDyString
@@ -36,7 +36,7 @@ void freeDyStringList(struct dyString **pDs);
 void dyStringAppend(struct dyString *ds, char *string);
 /* Append zero terminated string to end of dyString. */
 
-void dyStringAppendN(struct dyString *ds, char *string, int stringSize);
+void dyStringAppendN(struct dyString *ds, char *string, long stringSize);
 /* Append string of given size to end of string. */
 
 char dyStringAppendC(struct dyString *ds, char c);
@@ -77,7 +77,7 @@ struct dyString * dyStringSub(char *orig, char *in, char *out);
 /* Make up a duplicate of orig with all occurences of in substituted
  * with out. */
 
-void dyStringBumpBufSize(struct dyString *ds, int size);
+void dyStringBumpBufSize(struct dyString *ds, long size);
 /* Force dyString buffer to be at least given size. */
 
 char *dyStringCannibalize(struct dyString **pDy);
@@ -97,7 +97,7 @@ char *dyStringCannibalize(struct dyString **pDy);
 #define dyStringIsNotEmpty(ds) (ds->stringSize > 0)
 /* Return TRUE if dyString is not empty. */
 
-void dyStringResize(struct dyString *ds, int newSize);
+void dyStringResize(struct dyString *ds, long newSize);
 /* resize a string, if the string expands, blanks are appended */
 
 void dyStringQuoteString(struct dyString *dy, char quotChar, char *text);

src/inc/fieldedTable.h

@@ -36,6 +36,9 @@ void fieldedTableFree(struct fieldedTable **pTable);
 struct fieldedRow *fieldedTableAdd(struct fieldedTable *table,  char **row, int rowSize, int id);
 /* Create a new row and add it to table.  Return row. */
 
+struct fieldedRow *fieldedTableAddHead(struct fieldedTable *table, char **row, int rowSize, int id);
+/* Create a new row and add it to start of table.  Return row. */
+
 struct fieldedTable *fieldedTableFromTabFile(char *fileName, char *url, char *requiredFields[], int requiredCount);
 /* Read table from tab-separated file with a #header line that defines the fields.  Ensures
  * all requiredFields (if any) are present.  The url is just used for error reporting and 
@@ -45,6 +48,11 @@ struct fieldedTable *fieldedTableFromTabFile(char *fileName, char *url, char *re
 void fieldedTableToTabFile(struct fieldedTable *table, char *fileName);
 /* Write out a fielded table back to file */
 
+void fieldedTableToTabFileWithId(struct fieldedTable *table, char *fileName, 
+    char *idField, int startId);
+/* Write out a fielded table back to file.  If idField is non-NULL it will be added
+ * to the start of each output line as a steadily incrementing integer starting with startId. */
+
 boolean fieldedTableColumnIsNumeric(struct fieldedTable *table, int fieldIx);
 /* Return TRUE if field has numeric values wherever non-null */
 
@@ -57,6 +65,9 @@ void fieldedTableSortOnField(struct fieldedTable *table, char *field, boolean do
 int fieldedTableMustFindFieldIx(struct fieldedTable *table, char *field);
 /* Find index of field in table's row.  Abort if field not found. */
 
+int fieldedTableFindFieldIx(struct fieldedTable *table, char *field);
+/* Return index of field in a table's row or -1 if not found */
+
 struct hash *fieldedTableIndex(struct fieldedTable *table, char *field);
 /* Return hash of fieldedRows keyed by values of given field */
 

src/inc/genoFind.h

@@ -382,7 +382,7 @@ struct gfClump *gfPcrClumps(struct genoFind *gf,
 
 #define MAXSINGLEPIECESIZE 5000 /* maximum size of a single piece */
 
-#define gfVersion "36x2"	/* Current BLAT version number */
+#define gfVersion "36x4"	/* Current BLAT version number */
 
 #endif /* GENOFIND_H */