| b22faf0d |
#ifndef GMAPR_H
#define GMAPR_H
#include <Rinternals.h>
|
| 3f899953 |
/* .Call entry points for the gmapR package */
|
| b22faf0d |
SEXP
R_Bamread_new (SEXP bamfile_R);
SEXP
R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
|
| 4d5cc806 |
SEXP which_R, SEXP desired_read_group_R,
|
| b22faf0d |
SEXP alloclength_R,
SEXP minimum_mapq_R, SEXP good_unique_mapq_R,
SEXP maximum_nhits_R,
SEXP need_concordant_p_R, SEXP need_unique_p_R,
|
| 86afb162 |
SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,
|
| b22faf0d |
SEXP min_depth_R, SEXP variant_strands_R,
SEXP ignore_query_Ns_p,
SEXP print_indels_p_R,
SEXP blocksize_R,
|
| c78be696 |
SEXP verbosep_R, SEXP max_softclip_R,
|
| 8418591e |
SEXP genome_iit_file_R,
SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
|
| 685d60e3 |
SEXP minimum_quality_score_R, SEXP nonconvered_R,
SEXP print_nm_scores_p_R);
|
| b22faf0d |
|
| 3f899953 |
SEXP
R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
|
| c78be696 |
SEXP high_base_quality, SEXP which_R);
|
| 3f899953 |
|
| 86afb162 |
SEXP
R_Genome_getSeq (SEXP genome_dir_R, SEXP db_R,
SEXP seqnames_R, SEXP start_R, SEXP width_R, SEXP strand_R);
|
| b22faf0d |
#endif
|
