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new file mode 100644 |
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+.Rhistory |
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+*.o |
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+/src/gmap/Makefile |
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+/src/gmap/config.log |
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+/src/gmap/config.status |
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+/src/gmap/libtool |
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+/src/gmap/src/.deps/atoiindex-access.Po |
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+/src/gmap/src/.deps/atoiindex-assert.Po |
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+.deps |
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+/src/gmap/src/Makefile |
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+/src/gmap/src/atoiindex |
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+/src/gmap/src/cmetindex |
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+/src/gmap/src/config.h |
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+/src/gmap/src/get-genome |
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+/src/gmap/src/gmap |
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+/src/gmap/src/gmapindex |
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+/src/gmap/src/gmapl |
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+/src/gmap/src/gsnap |
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+/src/gmap/src/gsnapl |
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+/src/gmap/src/iit_dump |
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+/src/gmap/src/iit_get |
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+/src/gmap/src/iit_store |
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+/src/gmap/src/snpindex |
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+/src/gmap/src/stamp-h1 |
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+/src/gmap/src/uniqscan |
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+/src/gmap/src/uniqscanl |
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+/src/gmap/tests/Makefile |
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+/src/gmap/tests/align.test |
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| 29 |
+/src/gmap/tests/coords1.test |
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| 30 |
+/src/gmap/tests/iit.test |
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+/src/gmap/tests/setup1.test |
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| 32 |
+/src/gmap/util/Makefile |
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+/src/gmap/util/dbsnp_iit |
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+/src/gmap/util/dbsnp_iit.pl |
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+/src/gmap/util/fa_coords |
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+/src/gmap/util/fa_coords.pl |
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+/src/gmap/util/gff3_genes |
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+/src/gmap/util/gff3_genes.pl |
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+/src/gstruct/src/libgstruct_1.0_la-littleendian.lo |
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+src/gmap/util/gff3_introns |
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+src/gmap/util/gff3_introns.pl |
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+src/gmap/util/gff3_splicesites |
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+src/gmap/util/gff3_splicesites.pl |
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+src/gmap/util/gmap_build |
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+src/gmap/util/gmap_build.pl |
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+src/gmap/util/gmap_compress |
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+src/gmap/util/gmap_compress.pl |
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| 48 |
+src/gmap/util/gmap_process |
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| 49 |
+src/gmap/util/gmap_process.pl |
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| 50 |
+src/gmap/util/gmap_reassemble |
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| 51 |
+src/gmap/util/gmap_reassemble.pl |
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| 52 |
+src/gmap/util/gmap_setup |
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| 53 |
+src/gmap/util/gmap_setup.pl |
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+src/gmap/util/gmap_uncompress |
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+src/gmap/util/gmap_uncompress.pl |
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+src/gmap/util/gtf_genes |
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+src/gmap/util/gtf_genes.pl |
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| 58 |
+src/gmap/util/gtf_introns |
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+src/gmap/util/gtf_introns.pl |
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+src/gmap/util/gtf_splicesites |
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+src/gmap/util/gtf_splicesites.pl |
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+src/gmap/util/gvf_iit |
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+src/gmap/util/gvf_iit.pl |
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+src/gmap/util/md_coords |
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+src/gmap/util/md_coords.pl |
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| 66 |
+src/gmap/util/psl_genes |
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| 67 |
+src/gmap/util/psl_genes.pl |
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| 68 |
+src/gmap/util/psl_introns |
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+src/gmap/util/psl_introns.pl |
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+src/gmap/util/psl_splicesites |
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+src/gmap/util/psl_splicesites.pl |
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+src/gmap/util/vcf_iit |
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+src/gmap/util/vcf_iit.pl |
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| 74 |
+src/gmapR.so |
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| 75 |
+src/gstruct/Makefile |
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+src/gstruct/config.log |
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+src/gstruct/config.status |
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+src/gstruct/lib/gstruct-1.0.pc |
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+src/gstruct/libtool |
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+src/gstruct/src/.libs/ |
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+src/gstruct/src/Makefile |
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+src/gstruct/src/config.h |
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+src/gstruct/src/libgstruct-1.0.la |
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| 84 |
+src/gstruct/src/libgstruct_1.0_la-access.lo |
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| 85 |
+src/gstruct/src/libgstruct_1.0_la-assert.lo |
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+src/gstruct/src/libgstruct_1.0_la-bamread.lo |
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+src/gstruct/src/libgstruct_1.0_la-bamtally.lo |
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+src/gstruct/src/libgstruct_1.0_la-bigendian.lo |
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+src/gstruct/src/libgstruct_1.0_la-chrnum.lo |
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| 90 |
+src/gstruct/src/libgstruct_1.0_la-chrom.lo |
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| 91 |
+src/gstruct/src/libgstruct_1.0_la-datadir.lo |
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| 92 |
+src/gstruct/src/libgstruct_1.0_la-except.lo |
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| 93 |
+src/gstruct/src/libgstruct_1.0_la-genome.lo |
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| 94 |
+src/gstruct/src/libgstruct_1.0_la-genomicpos.lo |
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| 95 |
+src/gstruct/src/libgstruct_1.0_la-iit-read.lo |
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| 96 |
+src/gstruct/src/libgstruct_1.0_la-iit-write.lo |
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| 97 |
+src/gstruct/src/libgstruct_1.0_la-interval.lo |
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| 98 |
+src/gstruct/src/libgstruct_1.0_la-intlist.lo |
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| 99 |
+src/gstruct/src/libgstruct_1.0_la-list.lo |
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| 100 |
+src/gstruct/src/libgstruct_1.0_la-matchpool.lo |
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| 101 |
+src/gstruct/src/libgstruct_1.0_la-md5.lo |
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| 102 |
+src/gstruct/src/libgstruct_1.0_la-mem.lo |
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| 103 |
+src/gstruct/src/libgstruct_1.0_la-mismatchpool.lo |
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| 104 |
+src/gstruct/src/libgstruct_1.0_la-parserange.lo |
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| 105 |
+src/gstruct/src/libgstruct_1.0_la-samread.lo |
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| 106 |
+src/gstruct/src/libgstruct_1.0_la-sequence.lo |
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| 107 |
+src/gstruct/src/libgstruct_1.0_la-stopwatch.lo |
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| 108 |
+src/gstruct/src/libgstruct_1.0_la-table.lo |
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| 109 |
+src/gstruct/src/libgstruct_1.0_la-tableuint.lo |
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| 110 |
+src/gstruct/src/libgstruct_1.0_la-tally.lo |
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| 111 |
+src/gstruct/src/libgstruct_1.0_la-translation.lo |
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+src/gstruct/src/libgstruct_1.0_la-ucharlist.lo |
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+src/gstruct/src/libgstruct_1.0_la-uintlist.lo |
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+src/gstruct/src/libgstruct_1.0_la-uinttable.lo |
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| 115 |
+src/gstruct/src/stamp-h1 |
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+src/samtools/ |
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| 117 |
+inst/user |
| ... | ... |
@@ -10,7 +10,7 @@ |
| 10 | 10 |
cmetindex <- function(db, use_snps = NULL) {
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| 11 | 11 |
if (!is(db, "GmapGenome")) |
| 12 | 12 |
stop("'db' must be a GmapGenome object")
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| 13 |
- .cmetindex(genome(db), directory(db), directory(db), use_snps = use_snps) |
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| 13 |
+ .cmetindex(genome(db), directory(db), use_snps = use_snps) |
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| 14 | 14 |
} |
| 15 | 15 |
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| 16 | 16 |
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
