change -exons to -split. add tests that make sense.

src/fastaFromBed/fastaFromBedMain.cpp

@@ -88,7 +88,7 @@ int fastafrombed_main(int argc, char* argv[]) {
         else if(PARAMETER_CHECK("-name", 5, parameterLength)) {
             useNameOnly = true;
         }
-        else if(PARAMETER_CHECK("-exons", 6, parameterLength)) {
+        else if(PARAMETER_CHECK("-split", 6, parameterLength)) {
             useExons = true;
         }
         else if(PARAMETER_CHECK("-tab", 4, parameterLength)) {
@@ -131,7 +131,7 @@ void fastafrombed_help(void) {
     cerr << "\t-bed\tBED/GFF/VCF file of ranges to extract from -fi" << endl;
     cerr << "\t-fo\tOutput file (can be FASTA or TAB-delimited)" << endl;
     cerr << "\t-name\tUse the name field for the FASTA header" << endl;
-    cerr << "\t-exons\tgiven a bed12, concat the sequence from exons" << endl;
+    cerr << "\t-split\tgiven a bed12, concat the sequence from exons" << endl;
 
     cerr << "\t-tab\tWrite output in TAB delimited format." << endl;
     cerr << "\t\t- Default is FASTA format." << endl << endl;

test/fastaFromBed/blocks.bed

 chr1	0	40	three_blocks_match	0	+	0	0	0	3	2,10,10,	5,16,36,
+chr1	0	40	three_blocks_match	0	+	0	0	0	3	1,1,1,	10,20,30,

test/fastaFromBed/t.fa

 >chr1
-aaaaaaaaaa
-cccccccccc
-tttttttttt
-gggggggggg
-aaaaaaaaaa
+aggggggggg
+cggggggggg
+tggggggggg
+aggggggggg
+cggggggggg

test/fastaFromBed/test.sh

-echo $'chr1\t1\t10' | ./bin/bedtools getfasta -fi test/fastaFromBed/t.fa -bed stdin -fo t.txt
+echo $'chr1\t1\t10' | ../../bin/bedtools getfasta -fi t.fa -bed stdin -fo stdout > /dev/null
+
+LEN=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 2){ print length($0) }')
+
+if [ "$LEN" != "22" ]; then
+    print "BAD";
+fi
+
+SEQ=$(../../bin/bedtools getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 4){ print $0 }')
+
+if [ "$SEQ" != "cta" ]; then
+    print "BAD";
+fi
 
-./bin/bedtools getfasta -exons -fi test/fastaFromBed/t.fa -bed test/fastaFromBed/blocks.bed -fo stdout