314b81670d2d1446d4da81108ac0ce2a72fc569d
markd
  Fri Jan 6 15:32:57 2017 -0800
bigTransMap hgc working

diff --git src/hg/inc/bigTransMap.h src/hg/inc/bigTransMap.h
new file mode 100644
index 0000000..aafe4a0
--- /dev/null
+++ src/hg/inc/bigTransMap.h
@@ -0,0 +1,96 @@
+/* bigTransMap.h was originally generated by the autoSql program, which also 
+ * generated bigTransMap.c and bigTransMap.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BIGTRANSMAP_H
+#define BIGTRANSMAP_H
+
+#define BIGTRANSMAP_NUM_COLS 38
+
+extern char *bigTransMapCommaSepFieldNames;
+
+struct bigTransMap
+/* bigPsl derived pairwise alignment with additional information */
+    {
+    struct bigTransMap *next;  /* Next in singly linked list. */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    unsigned chromStart;	/* Start position in chromosome */
+    unsigned chromEnd;	/* End position in chromosome */
+    char *name;	/* Name or ID of item, ideally both human readable and unique */
+    unsigned score;	/* Score (0-1000), faction identity * 1000 */
+    char strand[2];	/* + or - indicates whether the query aligns to the + or - strand on the reference */
+    unsigned thickStart;	/* Start of where display should be thick (start codon) */
+    unsigned thickEnd;	/* End of where display should be thick (stop codon) */
+    unsigned reserved;	/* RGB value (use R,G,B string in input file) */
+    int blockCount;	/* Number of blocks */
+    int *blockSizes;	/* Comma separated list of block sizes */
+    int *chromStarts;	/* Start positions relative to chromStart */
+    unsigned oChromStart;	/* Start position in other chromosome */
+    unsigned oChromEnd;	/* End position in other chromosome */
+    char oStrand[2];	/* + or -, - means that psl was reversed into BED-compatible coordinates */
+    unsigned oChromSize;	/* Size of other chromosome. */
+    int *oChromStarts;	/* Start positions relative to oChromStart or from oChromStart+oChromSize depending on strand */
+    char *oSequence;	/* Sequence on other chrom (or edit list, or empty) */
+    char *oCDS;	/* CDS in NCBI format */
+    unsigned chromSize;	/* Size of target chromosome */
+    unsigned match;	/* Number of bases matched. */
+    unsigned misMatch;	/*  Number of bases that don't match  */
+    unsigned repMatch;	/*  Number of bases that match but are part of repeats  */
+    unsigned nCount;	/*  Number of 'N' bases  */
+    unsigned seqType;	/* 0=empty, 1=nucleotide, 2=amino_acid */
+    char *srcDb;	/* source organism database names */
+    char *srcChrom;	/* source organism chromosome name */
+    unsigned srcChromStart;	/* start position in source chromosome */
+    unsigned srcChromEnd;	/* end position in source chromosome */
+    unsigned srcScore;	/* source source (faction identity * 1000) */
+    unsigned srcAligned;	/* fraction of source aligned (faction identity * 1000) */
+    char *geneName;	/* gene name */
+    char *geneId;	/* gene identifier */
+    char *geneType;	/* type of gene */
+    char *transcriptType;	/* type of transcript */
+    char *chainType;	/* type of chains used for mapping */
+    char *commonName;	/* common organism name */
+    char *orgAbbrev;	/* organism abbreviation */
+    };
+
+struct bigTransMap *bigTransMapLoad(char **row);
+/* Load a bigTransMap from row fetched with select * from bigTransMap
+ * from database.  Dispose of this with bigTransMapFree(). */
+
+struct bigTransMap *bigTransMapLoadAll(char *fileName);
+/* Load all bigTransMap from whitespace-separated file.
+ * Dispose of this with bigTransMapFreeList(). */
+
+struct bigTransMap *bigTransMapLoadAllByChar(char *fileName, char chopper);
+/* Load all bigTransMap from chopper separated file.
+ * Dispose of this with bigTransMapFreeList(). */
+
+#define bigTransMapLoadAllByTab(a) bigTransMapLoadAllByChar(a, '\t');
+/* Load all bigTransMap from tab separated file.
+ * Dispose of this with bigTransMapFreeList(). */
+
+struct bigTransMap *bigTransMapCommaIn(char **pS, struct bigTransMap *ret);
+/* Create a bigTransMap out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigTransMap */
+
+void bigTransMapFree(struct bigTransMap **pEl);
+/* Free a single dynamically allocated bigTransMap such as created
+ * with bigTransMapLoad(). */
+
+void bigTransMapFreeList(struct bigTransMap **pList);
+/* Free a list of dynamically allocated bigTransMap's */
+
+void bigTransMapOutput(struct bigTransMap *el, FILE *f, char sep, char lastSep);
+/* Print out bigTransMap.  Separate fields with sep. Follow last field with lastSep. */
+
+#define bigTransMapTabOut(el,f) bigTransMapOutput(el,f,'\t','\n');
+/* Print out bigTransMap as a line in a tab-separated file. */
+
+#define bigTransMapCommaOut(el,f) bigTransMapOutput(el,f,',',',');
+/* Print out bigTransMap as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* BIGTRANSMAP_H */
+