Clarify how defaults work when building an index with tabix

tabix.1

@@ -87,17 +87,17 @@ Specify that the position in the data file is 0-based half-open
 (e.g. UCSC files) rather than 1-based.
 .TP
 .BI "-b, --begin " INT
-Column of start chromosomal position. [4]
+Column of start chromosomal position.
 .TP
 .BI "-c, --comment " CHAR
-Skip lines started with character CHAR. [#]
+Skip lines started with character CHAR.
 .TP
 .BI "-C, --csi"
 Produce CSI format index instead of classical tabix or BAI style indices.
 .TP
 .BI "-e, --end " INT
 Column of end chromosomal position. The end column can be the same as the
-start column. [5]
+start column.
 .TP
 .B "-f, --force "
 Force to overwrite the index file if it is present.
@@ -110,15 +110,15 @@ Input format for indexing. Valid values are: gff, bed, sam, vcf.
 This option should not be applied together with any of
 .BR -s ", " -b ", " -e ", " -c " and " -0 ;
 it is not used for data retrieval because this setting is stored in
-the index file. [gff]
+the index file.
 .TP
 .BI "-s, --sequence " INT
 Column of sequence name. Option
 .BR -s ", " -b ", " -e ", " -S ", " -c " and " -0
-are all stored in the index file and thus not used in data retrieval. [1]
+are all stored in the index file and thus not used in data retrieval.
 .TP
 .BI "-S, --skip-lines " INT
-Skip first INT lines in the data file. [0]
+Skip first INT lines in the data file.
 
 .SH QUERYING AND OTHER OPTIONS
 .TP
@@ -173,6 +173,25 @@ Values higher than 3 produce additional informational and debugging messages.
 .BI "-@, --threads " INT
 Set number of threads to use for the operation.
 The default is 0, where no extra threads are in use.
+.PP
+Unless one of the options
+.BR -0 ,
+.BR -b ,
+.BR -c ,
+.BR -e ,
+.BR -p ,
+.BR -s ,
+or
+.B -S
+is used when building an index,
+tabix will attempt to set its configuration by detecting the file type being
+indexed.
+If detection fails, or any of the options above is present,
+the settings used will be those for the gff preset unless overridden
+.br
+i.e. one-based positions,
+.B -s 1 -b 4 -e 5 -c '#' -S 0
+
 .PP
 .SH EXAMPLE
 (grep "^#" in.gff; grep -v "^#" in.gff | sort -t"`printf '\(rst'`" -k1,1 -k4,4n) | bgzip > sorted.gff.gz;

tabix.c

@@ -585,15 +585,15 @@ static int usage(FILE *fp, int status)
     fprintf(fp, "\n");
     fprintf(fp, "Indexing Options:\n");
     fprintf(fp, "   -0, --zero-based           coordinates are zero-based\n");
-    fprintf(fp, "   -b, --begin INT            column number for region start [4]\n");
-    fprintf(fp, "   -c, --comment CHAR         skip comment lines starting with CHAR [null]\n");
+    fprintf(fp, "   -b, --begin INT            column number for region start\n");
+    fprintf(fp, "   -c, --comment CHAR         skip comment lines starting with CHAR\n");
     fprintf(fp, "   -C, --csi                  generate CSI index for VCF (default is TBI)\n");
-    fprintf(fp, "   -e, --end INT              column number for region end (if no end, set INT to -b) [5]\n");
+    fprintf(fp, "   -e, --end INT              column number for region end (if no end, set INT to -b)\n");
     fprintf(fp, "   -f, --force                overwrite existing index without asking\n");
     fprintf(fp, "   -m, --min-shift INT        set minimal interval size for CSI indices to 2^INT [14]\n");
     fprintf(fp, "   -p, --preset STR           gff, bed, sam, vcf, gaf\n");
-    fprintf(fp, "   -s, --sequence INT         column number for sequence names (suppressed by -p) [1]\n");
-    fprintf(fp, "   -S, --skip-lines INT       skip first INT lines [0]\n");
+    fprintf(fp, "   -s, --sequence INT         column number for sequence names (suppressed by -p)\n");
+    fprintf(fp, "   -S, --skip-lines INT       skip first INT lines\n");
     fprintf(fp, "\n");
     fprintf(fp, "Querying and other options:\n");
     fprintf(fp, "   -h, --print-header         print also the header lines\n");
@@ -608,6 +608,11 @@ static int usage(FILE *fp, int status)
     fprintf(fp, "       --verbosity INT        set verbosity [3]\n");
     fprintf(fp, "   -@, --threads INT          number of additional threads to use [0]\n");
     fprintf(fp, "\n");
+    fprintf(fp, "Unless one of the options -0, -b, -c, -e, -p, -s, or -S is used when building\n");
+    fprintf(fp, "an index, tabix will attempt to set its configuration by detecting the file\n");
+    fprintf(fp, "type being indexed.  If detection fails, or any of the options above is present,\n");
+    fprintf(fp, "the settings used will be those for the gff preset unless overridden\n");
+    fprintf(fp, "i.e. one-based positions, -s 1 -b 4 -e 5 -c '#' -S 0\n");
     return status;
 }