Added support for pre-defined column defn's (e.g., sam, bed, vcf)

nawk/addon.c

@@ -1,36 +1,172 @@
 #include <ctype.h>
 #include <stdio.h>
+#include <string.h>
 #include "awk.h"
 #include "addon.h"
 
-int lh3_has_colnm = 0;
+const char *lh3_col_defn = NULL;
+const char *valid_coldefs[] = {"header", "bed", "bedgraph", "sam", "vcf", "gff", NULL};
+
+/*BED*/
+const char *bed_coldefs[] = {"chrom", "start", "end", 
+                             "name", "score", "strand", 
+                             "thickstart", "thickend", "rgb",
+                             "blockcount", "blocksizes", "blockstarts",
+                              NULL};
+/*BEDGRAPH*/
+const char *bedgraph_coldefs[] = {"chrom", "start", "end", "score", NULL};
+/*SAM*/
+const char *sam_coldefs[] = {"qname", "flag", "rname",
+                             "pos", "mapq", "cigar",
+                             "rnext", "pnext", "tlen",
+                             "seq", "qual", NULL};
+/*VCF*/
+const char *vcf_coldefs[] = {"chrom", "pos", "id",
+                             "ref", "alt", "qual",
+                             "filter" "info", NULL};
+/*GFF/GTF*/
+const char *gff_coldefs[] = {"seqname", "source", "feature", 
+                             "start", "end", "score",
+                             "filter", "strand", "group",
+                             "attribute", NULL};
 
 static void set_colnm_aux(const char *p, int col)
 {
-	const char *q;
-	Cell *x;
-	for (q = p; *q; ++q)
-		if (!isdigit(*q)) break;
-	if (*q == 0) return; /* do not set if string p is an integer */
-	if ((x = lookup(p, symtab)) != NULL)
-		x->tval = NUM, x->fval = col;
+    const char *q;
+    Cell *x;
+    for (q = p; *q; ++q)
+        if (!isdigit(*q)) break;
+    if (*q == 0) return; /* do not set if string p is an integer */
+    if ((x = lookup(p, symtab)) != NULL)
+        x->tval = NUM, x->fval = col;
+}
+
+int isvalid_coldef(const char *request)
+{
+    int i;
+    for (i = 0; valid_coldefs[i] != NULL; ++i)
+        if (strcmp(request, valid_coldefs[i]) == 0)
+            return 1;
+    return 0;
+}
+
+void print_valid_coldefs() 
+{
+    printf("valid -c options include:\n");
+    int i;
+    for (i = 0; valid_coldefs[i] != NULL; ++i)
+    {
+        const char *option = valid_coldefs[i];
+        printf("  %d. \"%s\"\n", i+1,option);
+
+        if (strcmp(option, "header") == 0)
+            printf("    input should contain a col. defn header as first line\n");
+        else if (strcmp(option, "bed") == 0) {
+            int j;
+            for (j = 0; bed_coldefs[j] != NULL; ++j)
+                printf("    %s: column $%d\n", bed_coldefs[j], j+1);
+        }
+        else if (strcmp(option, "bedgraph") == 0) {
+            int j;
+            for (j = 0; bedgraph_coldefs[j] != NULL; ++j)
+                printf("    %s: column $%d\n", bedgraph_coldefs[j], j+1);
+        }
+        else if (strcmp(option, "sam") == 0) {
+            int j;
+            for (j = 0; sam_coldefs[j] != NULL; ++j)
+                printf("    %s: column $%d\n", sam_coldefs[j], j+1);
+        }
+        else if (strcmp(option, "vcf") == 0) {
+            int j;
+            for (j = 0; vcf_coldefs[j] != NULL; ++j)
+                printf("    %s: column $%d\n", vcf_coldefs[j], j+1);
+        }
+        else if (strcmp(option, "gff") == 0) {
+            int j;
+            for (j = 0; gff_coldefs[j] != NULL; ++j)
+                if (strcmp(gff_coldefs[j], "attribute") != 0)
+                    printf("    %s: column $%d\n", gff_coldefs[j], j+1);
+                else
+                    printf("    %s: column $%d\n", gff_coldefs[j], j);
+        }
+    }
 }
 
 void lh3_set_colnm()
 {
-	char *p, *q, c;
-	int i;
-	if (lh3_has_colnm == 0) return;
-	for (p = record; *p && isspace(*p); ++p); /* skip leading spaces */
-	for (i = 1, q = p; *q; ++q) {
-		if (!isspace(*q)) continue;
-		c = *q; /* backup the space */
-		*q = 0; /* terminate the field */
-		set_colnm_aux(p, i);
-		*q = c; /* change back */
-		++i;
-		for (p = q + 1; *p && isspace(*p); ++p); /* skip contiguous spaces */
-		q = p;
-	}
-	set_colnm_aux(p, i); /* the last column */
+    if (lh3_col_defn == NULL) return;
+
+    if (strcmp(lh3_col_defn, "header") == 0) {
+        char *p, *q, c;
+        int i;
+        for (p = record; *p && isspace(*p); ++p); /* skip leading spaces */
+        for (i = 1, q = p; *q; ++q) {
+            if (!isspace(*q)) continue;
+            c = *q; /* backup the space */
+            *q = 0; /* terminate the field */
+            set_colnm_aux(p, i);
+            *q = c; /* change back */
+            ++i;
+            for (p = q + 1; *p && isspace(*p); ++p); /* skip contiguous spaces */
+            q = p;
+        }
+        set_colnm_aux(p, i); /* the last column */
+    } 
+    else if (strcmp(lh3_col_defn, "bed") == 0) {
+        int i;
+        for (i = 0; bed_coldefs[i] != NULL; ++i)
+            set_colnm_aux(bed_coldefs[i], i+1);
+        // force tab delimited input and output
+        *FS = "\t";
+        *OFS = "\t";
+    }
+    else if (strcmp(lh3_col_defn, "bedgraph") == 0) {
+        int i;
+        for (i = 0; bedgraph_coldefs[i] != NULL; ++i)
+            set_colnm_aux(bedgraph_coldefs[i], i+1);
+        // force tab delimited input and output
+        *FS = "\t";
+        *OFS = "\t";
+    }
+    else if (strcmp(lh3_col_defn, "sam") == 0) {
+        int i;
+        for (i = 0; sam_coldefs[i] != NULL; ++i)
+            set_colnm_aux(sam_coldefs[i], i+1);
+        // force tab delimited input and output
+        *FS = "\t";
+        *OFS = "\t";
+        // auto-report any header lines
+        while (getrec(&record, &recsize, 1) > 0 && record[0] == '@') {
+            printf("%s\n", record);
+        }
+    }
+    else if (strcmp(lh3_col_defn, "vcf") == 0) {
+        int i;
+        for (i = 0; vcf_coldefs[i] != NULL; ++i)
+            set_colnm_aux(vcf_coldefs[i], i+1);
+        // todo: any intelligent way to handle genotypes?
+        // force tab delimited input and output
+        *FS = "\t";
+        *OFS = "\t";
+        // auto-report any header lines
+        while (getrec(&record, &recsize, 1) > 0 && record[0] == '#') {
+            printf("%s\n", record);
+        }
+    }
+    else if (strcmp(lh3_col_defn, "gff") == 0 || strcmp(lh3_col_defn, "gtf") == 0) {
+        int i;
+        for (i = 0; gff_coldefs[i] != NULL; ++i)
+            // allow "group" and "attribute" to be the ninth column
+            if (strcmp(lh3_col_defn, "attribute") != 0)
+                set_colnm_aux(gff_coldefs[i], i+1);
+            else
+                set_colnm_aux(gff_coldefs[i], i);
+        // force tab delimited input and output
+        *FS = "\t";
+        *OFS = "\t";
+        // auto-report any header lines
+        while (getrec(&record, &recsize, 1) > 0 && record[0] == '#') {
+            printf("%s\n", record);
+        }
+    }
 }

nawk/addon.h

@@ -1,7 +1,16 @@
 #ifndef ADDON_H
 #define ADDON_H
 
-extern int lh3_has_colnm;
-void lh3_set_colnm();
+//extern int lh3_has_colnm;
+
+/* column definition, "header" reads frist line  
+   other current options include:
+     bed, bedgraph, sam, vcf
+*/
+extern const char *lh3_col_defn;   
+
+void lh3_set_colnm();             /* assoc. col names w/ numbers */ 
+int isvalid_coldef(const char *); /* is the req. col defn. valid? */
+void print_valid_coldefs();       /* print a list of supported col defns. */
 
 #endif

nawk/main.c

@@ -58,7 +58,7 @@ int	safe	= 0;	/* 1 => "safe" mode */
 int main(int argc, char *argv[])
 {
 	const char *fs = NULL;
-
+	
 	setlocale(LC_CTYPE, "");
 	setlocale(LC_NUMERIC, "C"); /* for parsing cmdline & prog */
 	cmdname = argv[0];
@@ -144,7 +144,19 @@ int main(int argc, char *argv[])
 			printf("awk %s\n", version);
 			break;
 		case 'c':
-			lh3_has_colnm = 1;
+			if (argv[1][2] != 0) {	/* arg is -csomething */
+				lh3_col_defn = &argv[1][2];
+			} else {		/* arg is -c something */
+				argc--; argv++;
+				if (argc <= 1)
+					FATAL("no variable name");
+				if (!isvalid_coldef(argv[1]) || strcmp(argv[1], "help") == 0) {
+				    print_valid_coldefs();
+                    exit(1);
+                }
+				else
+                    lh3_col_defn = argv[1];
+			}
 			break;
 		default:
 			WARNING("unknown option %s ignored", argv[1]);

nawk/run.c

@@ -189,7 +189,7 @@ Cell *program(Node **a, int n)	/* execute an awk program */
 	}
 	if (a[1] || a[2])
 		while (getrec(&record, &recsize, 1) > 0) {
-			if (lh3_has_colnm && (int)(*NR + .499) == 1) lh3_set_colnm();
+			if (lh3_col_defn != NULL && (int)(*NR + .499) == 1) lh3_set_colnm();
 			x = execute(a[1]);
 			if (isexit(x))
 				break;