9ed6f979a8ec95ac934e5e8fef028d188b76a035
chmalee
  Mon Aug 6 14:38:57 2018 -0700
pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079

diff --git src/hg/inc/txAliDiff.h src/hg/inc/txAliDiff.h
new file mode 100644
index 0000000..90a2b62
--- /dev/null
+++ src/hg/inc/txAliDiff.h
@@ -0,0 +1,82 @@
+/* txAliDiff.h was originally generated by the autoSql program, which also 
+ * generated txAliDiff.c and txAliDiff.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef TXALIDIFF_H
+#define TXALIDIFF_H
+
+#define TXALIDIFF_NUM_COLS 20
+
+extern char *txAliDiffCommaSepFieldNames;
+
+struct txAliDiff
+/* Differences between reference genome and transcript sequences */
+    {
+    struct txAliDiff *next;  /* Next in singly linked list. */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    unsigned chromStart;	/* Start position in chromosome of ambiguous gap placement region */
+    unsigned chromEnd;	/* End position in chromosome of ambiguous gap placement region */
+    char *name;	/* Name of item */
+    unsigned score;	/* Not used */
+    char strand[2];	/* Transcript orientation on genome: + or - */
+    unsigned thickStart;	/* Start position of 3'-most location for gaps that can shift position without introducing mismatches */
+    unsigned thickEnd;	/* End position of 3'-most gap location for gaps that can shift position without introducing mismatches */
+    unsigned reserved;	/* RGB color of this item */
+    char *txName;	/* Transcript identifier */
+    unsigned txStart;	/* Start position in transcript (of ambiguous gap placement region where applicable) */
+    unsigned txEnd;	/* End position in transcript (of ambiguous gap placement region where applicable) */
+    unsigned gSkipped;	/* Number of bases skipped on genome, if any */
+    unsigned txSkipped;	/* Number of bases skipped on transcript, if any */
+    unsigned shiftL;	/* Number of bases that gap can be shifted left on genome with no mismatches */
+    unsigned shiftR;	/* Number of bases that gap can be shifted right on genome with no mismatches */
+    char *hgvsG;	/* HGVS g. notation of genome change to match transcript */
+    char *hgvsCN;	/* HGVS c./n. notation of part of transcript not matched in genome */
+    char *hgvsN;	/* HGVS c./n. notation of transcript change to match genome */
+    char *hgvsPosCN;	/* HGVS c./n. position range of transcript ambiguous gap placement region */
+    };
+
+void txAliDiffStaticLoad(char **row, struct txAliDiff *ret);
+/* Load a row from txAliDiff table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct txAliDiff *txAliDiffLoad(char **row);
+/* Load a txAliDiff from row fetched with select * from txAliDiff
+ * from database.  Dispose of this with txAliDiffFree(). */
+
+struct txAliDiff *txAliDiffLoadAll(char *fileName);
+/* Load all txAliDiff from whitespace-separated file.
+ * Dispose of this with txAliDiffFreeList(). */
+
+struct txAliDiff *txAliDiffLoadAllByChar(char *fileName, char chopper);
+/* Load all txAliDiff from chopper separated file.
+ * Dispose of this with txAliDiffFreeList(). */
+
+#define txAliDiffLoadAllByTab(a) txAliDiffLoadAllByChar(a, '\t');
+/* Load all txAliDiff from tab separated file.
+ * Dispose of this with txAliDiffFreeList(). */
+
+struct txAliDiff *txAliDiffCommaIn(char **pS, struct txAliDiff *ret);
+/* Create a txAliDiff out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new txAliDiff */
+
+void txAliDiffFree(struct txAliDiff **pEl);
+/* Free a single dynamically allocated txAliDiff such as created
+ * with txAliDiffLoad(). */
+
+void txAliDiffFreeList(struct txAliDiff **pList);
+/* Free a list of dynamically allocated txAliDiff's */
+
+void txAliDiffOutput(struct txAliDiff *el, FILE *f, char sep, char lastSep);
+/* Print out txAliDiff.  Separate fields with sep. Follow last field with lastSep. */
+
+#define txAliDiffTabOut(el,f) txAliDiffOutput(el,f,'\t','\n');
+/* Print out txAliDiff as a line in a tab-separated file. */
+
+#define txAliDiffCommaOut(el,f) txAliDiffOutput(el,f,',',',');
+/* Print out txAliDiff as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* TXALIDIFF_H */
+