4c9ae67ea6e03ec3069cea012398793046e9ff2a
giardine
  Tue Sep 21 15:00:29 2010 -0700
Adds new track type bedDetail to custom and resident tracks, also adds pgSnp (personal genome SNPs) as custom track type.  bedDetail is bed4 to bed12, with 2 extra fields for an ID and description for hgc clicks.
diff --git src/hg/lib/bedDetail.c src/hg/lib/bedDetail.c
new file mode 100644
index 0000000..48a32a4
--- /dev/null
+++ src/hg/lib/bedDetail.c
@@ -0,0 +1,312 @@
+/* bedDetail.c was originally generated by the autoSql program, which also 
+ * generated bedDetail.h and bedDetail.sql.  This module links the database and
+ * the RAM representation of objects. */
+
+#include "common.h"
+#include "linefile.h"
+#include "dystring.h"
+#include "jksql.h"
+#include "basicBed.h"
+#include "bedDetail.h"
+
+static char const rcsid[] = "$Id:$";
+
+struct bedDetail *bedDetailLoad(char **row)
+/* Load a bedDetail from row fetched with select * from bedDetail
+ * from database.  Dispose of this with bedDetailFree(). */
+{
+struct bedDetail *ret;
+
+AllocVar(ret);
+ret->blockCount = sqlSigned(row[9]);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+ret->score = sqlUnsigned(row[4]);
+safecpy(ret->strand, sizeof(ret->strand), row[5]);
+ret->thickStart = sqlUnsigned(row[6]);
+ret->thickEnd = sqlUnsigned(row[7]);
+ret->reserved = sqlUnsigned(row[8]);
+{
+int sizeOne;
+sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+{
+int sizeOne;
+sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
+assert(sizeOne == ret->blockCount);
+}
+ret->id = cloneString(row[12]);
+ret->description = cloneString(row[13]);
+return ret;
+}
+
+struct bedDetail *bedDetailLoadAll(char *fileName) 
+/* Load all bedDetail from a whitespace-separated file.
+ * Dispose of this with bedDetailFreeList(). */
+{
+struct bedDetail *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileRow(lf, row))
+    {
+    el = bedDetailLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bedDetail *bedDetailLoadAllByChar(char *fileName, char chopper) 
+/* Load all bedDetail from a chopper separated file.
+ * Dispose of this with bedDetailFreeList(). */
+{
+struct bedDetail *list = NULL, *el;
+struct lineFile *lf = lineFileOpen(fileName, TRUE);
+char *row[14];
+
+while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
+    {
+    el = bedDetailLoad(row);
+    slAddHead(&list, el);
+    }
+lineFileClose(&lf);
+slReverse(&list);
+return list;
+}
+
+struct bedDetail *bedDetailCommaIn(char **pS, struct bedDetail *ret)
+/* Create a bedDetail out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bedDetail */
+{
+char *s = *pS;
+
+if (ret == NULL)
+    AllocVar(ret);
+ret->chrom = sqlStringComma(&s);
+ret->chromStart = sqlUnsignedComma(&s);
+ret->chromEnd = sqlUnsignedComma(&s);
+ret->name = sqlStringComma(&s);
+ret->score = sqlUnsignedComma(&s);
+sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
+ret->thickStart = sqlUnsignedComma(&s);
+ret->thickEnd = sqlUnsignedComma(&s);
+ret->reserved = sqlUnsignedComma(&s);
+ret->blockCount = sqlSignedComma(&s);
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->blockSizes, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->blockSizes[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+{
+int i;
+s = sqlEatChar(s, '{');
+AllocArray(ret->chromStarts, ret->blockCount);
+for (i=0; i<ret->blockCount; ++i)
+    {
+    ret->chromStarts[i] = sqlSignedComma(&s);
+    }
+s = sqlEatChar(s, '}');
+s = sqlEatChar(s, ',');
+}
+ret->id = sqlStringComma(&s);
+ret->description = sqlStringComma(&s);
+*pS = s;
+return ret;
+}
+
+void bedDetailFree(struct bedDetail **pEl)
+/* Free a single dynamically allocated bedDetail such as created
+ * with bedDetailLoad(). */
+{
+struct bedDetail *el;
+
+if ((el = *pEl) == NULL) return;
+freeMem(el->chrom);
+freeMem(el->name);
+freeMem(el->blockSizes);
+freeMem(el->chromStarts);
+freeMem(el->id);
+freeMem(el->description);
+freez(pEl);
+}
+
+void bedDetailFreeList(struct bedDetail **pList)
+/* Free a list of dynamically allocated bedDetail's */
+{
+struct bedDetail *el, *next;
+
+for (el = *pList; el != NULL; el = next)
+    {
+    next = el->next;
+    bedDetailFree(&el);
+    }
+*pList = NULL;
+}
+
+void bedDetailOutput(struct bedDetail *el, FILE *f, char sep, char lastSep, int size) 
+/* Print out bedDetail.  Separate fields with sep. Follow last field with lastSep. */
+{
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->chrom);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+fprintf(f, "%u", el->chromStart);
+fputc(sep,f);
+fprintf(f, "%u", el->chromEnd);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->name);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (size > 6)
+    {
+    fprintf(f, "%u", el->score);
+    fputc(sep,f);
+    }
+if (size > 7)
+    {
+    if (sep == ',') fputc('"',f);
+    fprintf(f, "%s", el->strand);
+    if (sep == ',') fputc('"',f);
+    fputc(sep,f);
+    }
+if (size > 8)
+    {
+    fprintf(f, "%u", el->thickStart);
+    fputc(sep,f);
+    }
+if (size > 9)
+    {
+    fprintf(f, "%u", el->thickEnd);
+    fputc(sep,f);
+    }
+if (size > 10)
+    {
+    fprintf(f, "%u", el->reserved);
+    fputc(sep,f);
+    }
+if (size > 11)
+    {
+    fprintf(f, "%d", el->blockCount);
+    fputc(sep,f);
+    }
+if (size > 12)
+    {
+    int i;
+    if (sep == ',') fputc('{',f);
+    for (i=0; i<el->blockCount; ++i)
+        {
+        fprintf(f, "%d", el->blockSizes[i]);
+        fputc(',', f);
+        }
+    if (sep == ',') fputc('}',f);
+    fputc(sep,f);
+    }
+if (size > 13) 
+    {
+    int i;
+    if (sep == ',') fputc('{',f);
+    for (i=0; i<el->blockCount; ++i)
+        {
+        fprintf(f, "%d", el->chromStarts[i]);
+        fputc(',', f);
+        }
+    if (sep == ',') fputc('}',f);
+    fputc(sep,f);
+    }
+/* last 2 should always be present */
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->id);
+if (sep == ',') fputc('"',f);
+fputc(sep,f);
+if (sep == ',') fputc('"',f);
+fprintf(f, "%s", el->description);
+if (sep == ',') fputc('"',f);
+fputc(lastSep,f);
+}
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+char *bedDetailAutoSqlString =
+"table bedDetail\n"
+"\"Browser extensible data, with extended fields for detail page\"\n"
+"   (\n"
+"   string chrom;      \"Reference sequence chromosome or scaffold\"\n"
+"   uint   chromStart; \"Start position in chromosome\"\n"
+"   uint   chromEnd;   \"End position in chromosome\"\n"
+"   string name;       \"Short Name of item\"\n"
+"   uint   score;      \"Score from 0-1000\"\n"
+"   char[1] strand;    \"+ or -\"\n"
+"   uint thickStart;   \"Start of where display should be thick (start codon)\"\n"
+"   uint thickEnd;     \"End of where display should be thick (stop codon)\"\n"
+"   uint reserved;     \"Used as itemRgb as of 2004-11-22\"\n"
+"   int blockCount;    \"Number of blocks\"\n"
+"   int[blockCount] blockSizes; \"Comma separated list of block sizes\"\n"
+"   int[blockCount] chromStarts; \"Start positions relative to chromStart\"\n"
+"   uint expCount;     \"Number of experiment values\"\n"
+"   int[expCount] expIds; \"Comma separated list of experiment IDs\"\n"
+"   float[expCount] expScores; \"Comma separated list of experiment scores\"\n"
+"   string id;         \"ID to bed used in URL to link back\"\n"
+"   lstring description; \"Long description of item for the details page\"\n"
+"   )\n"
+;
+
+struct bedDetail *bedDetailLoadWithGaps(char **row, int size)
+/* Load a bedDetail from row split from a file or from database, 
+   may have parts of BED not included.  Dispose of this with bedDetailFree(). 
+   Size is total number of fields 
+*/
+{
+struct bedDetail *ret;
+AllocVar(ret);
+ret->chrom = cloneString(row[0]);
+ret->chromStart = sqlUnsigned(row[1]);
+ret->chromEnd = sqlUnsigned(row[2]);
+ret->name = cloneString(row[3]);
+if (size > 6 && row[4] != NULL)
+    ret->score = sqlUnsigned(row[4]);
+if (size > 7 && row[5] != NULL) 
+    safecpy(ret->strand, sizeof(ret->strand), row[5]);
+if (size > 8 && row[6] != NULL)
+    ret->thickStart = sqlUnsigned(row[6]);
+if (size > 9 && row[7] != NULL)
+    ret->thickEnd = sqlUnsigned(row[7]);
+if (size > 10 && row[8] != NULL)
+    {
+    char *comma = strchr(row[8], ',');
+    if (comma)
+        ret->reserved = bedParseRgb(row[8]);
+    else
+        ret->reserved = 0;
+    }
+if (size > 11 && row[9] != NULL)
+    ret->blockCount = sqlSigned(row[9]);
+if (size > 12 && row[10] != NULL)
+    {
+    int sizeOne;
+    sqlSignedDynamicArray(row[10], &ret->blockSizes, &sizeOne);
+    assert(sizeOne == ret->blockCount);
+    }
+if (size > 13 && row[11] != NULL)
+    {
+    int sizeOne;
+    sqlSignedDynamicArray(row[11], &ret->chromStarts, &sizeOne);
+    assert(sizeOne == ret->blockCount);
+    }
+/* these 2 should not be null, but always last 2 */
+ret->id = cloneString(row[size-2]);
+ret->description = cloneString(row[size-1]);
+return ret;
+}