Commit eaab251e authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.0+git20180904.0e87e322+dfsg

parent e05aad85

src/inc/bwgInternal.h

+1 −1
Original line number Diff line number Diff line
@@ -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

+5 −5
Original line number Diff line number Diff line
@@ -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

+8 −2
Original line number Diff line number Diff line
@@ -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

+1 −1
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/*****************************************************************************

 * 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

+1 −1
Original line number Diff line number Diff line 
/* 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"