1. gmapR
  2. src
  3. gmapR.h
Browse code

support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
Showing 1 changed files
src/gmapR.h
History View file @ c3db7e3
... ... 
@@ -16,14 +16,14 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
16 16 
                 SEXP maximum_nhits_R,
17 17 
                 SEXP need_concordant_p_R, SEXP need_unique_p_R,
18 18 
                 SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,
19 
-                SEXP min_depth_R, SEXP variant_strands_R,
20 
-                SEXP ignore_query_Ns_p,
19 
+                SEXP min_depth_R, SEXP variant_strands_R, SEXP variant_pct_R,
20 
+                SEXP ignore_query_Ns_p_R,
21 21 
                 SEXP print_indels_p_R,
22 22 
                 SEXP blocksize_R,
23 
-                SEXP verbosep_R, SEXP max_softclip_R,
24 
-                SEXP genome_iit_file_R,
23 
+                SEXP verbosep_R, SEXP min_softclip_R, SEXP max_softclip_R,
24 
+                SEXP exon_iit_file_R,
25 25 
                 SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
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-                SEXP minimum_quality_score_R, SEXP nonconvered_R,
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+                SEXP minimum_quality_score_R, SEXP noncovered_R,
27 27 
                 SEXP print_nm_scores_p_R);
28 28
29 29 
 SEXP
Browse code

work towards supporting new bam_tally; drops quality info (now cutoff based), adds xs/nm/del and codon-level counts

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110593 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/11/2015 21:50:11
Showing 1 changed files
src/gmapR.h
History View file @ 685d60e
... ... 
@@ -23,7 +23,8 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
23 23 
                 SEXP verbosep_R, SEXP max_softclip_R,
24 24 
                 SEXP genome_iit_file_R,
25 25 
                 SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
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-                SEXP minimum_quality_score_R, SEXP nonconvered_R);
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+                SEXP minimum_quality_score_R, SEXP nonconvered_R,
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+                SEXP print_nm_scores_p_R);
27 28
28 29 
 SEXP
29 30 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
Browse code

resurrect improvements that we reverted before the April release, expect breakage for a while

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110039 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2015 18:51:00
Showing 1 changed files
src/gmapR.h
History View file @ 8418591
... ... 
@@ -21,7 +21,9 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
21 21 
                 SEXP print_indels_p_R,
22 22 
                 SEXP blocksize_R,
23 23 
                 SEXP verbosep_R, SEXP max_softclip_R,
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-		SEXP genome_iit_file_R);
24 
+                SEXP genome_iit_file_R,
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+                SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
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+                SEXP minimum_quality_score_R, SEXP nonconvered_R);
25 27
26 28 
 SEXP
27 29 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
Browse code

Reverted to r101133, along with NAMESPACE fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102487 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:40:44
Showing 1 changed files
src/gmapR.h
History View file @ d5ed124
... ... 
@@ -21,9 +21,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
21 21 
                 SEXP print_indels_p_R,
22 22 
                 SEXP blocksize_R,
23 23 
                 SEXP verbosep_R, SEXP max_softclip_R,
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-                SEXP genome_iit_file_R,
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-                SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
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-                SEXP minimum_quality_score_R, SEXP nonconvered_R);
24 
+		SEXP genome_iit_file_R);
27 25
28 26 
 SEXP
29 27 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
Browse code

Recent work towards supporting the new features... will revert back to a stable version immediately...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102485 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:32:10
Showing 1 changed files
src/gmapR.h
History View file @ c8fd96e
... ... 
@@ -21,7 +21,9 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
21 21 
                 SEXP print_indels_p_R,
22 22 
                 SEXP blocksize_R,
23 23 
                 SEXP verbosep_R, SEXP max_softclip_R,
24 
-		SEXP genome_iit_file_R);
24 
+                SEXP genome_iit_file_R,
25 
+                SEXP print_xs_scores_p_R, SEXP print_cycles_p_R,
26 
+                SEXP minimum_quality_score_R, SEXP nonconvered_R);
25 27
26 28 
 SEXP
27 29 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
Browse code

add codon tally support. No vbump yet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 11/08/2014 23:42:48
Showing 1 changed files
src/gmapR.h
History View file @ c78be69
... ... 
@@ -20,12 +20,12 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
20 20 
                 SEXP ignore_query_Ns_p,
21 21 
                 SEXP print_indels_p_R,
22 22 
                 SEXP blocksize_R,
23 
-                SEXP verbosep_R, SEXP max_softclip_R, SEXP print_xs_scores_p_R,
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-                SEXP noncovered_R);
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+                SEXP verbosep_R, SEXP max_softclip_R,
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+		SEXP genome_iit_file_R);
25 25
26 26 
 SEXP
27 27 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
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-                  SEXP high_base_quality, SEXP which_R, SEXP xs_R);
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+                  SEXP high_base_quality, SEXP which_R);
29 29
30 30 
 SEXP
31 31 
 R_Genome_getSeq (SEXP genome_dir_R, SEXP db_R,
Browse code

update to new bam_tally with support for XS counting, which we now support via BamTallyParam@count_xs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@90225 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 13/05/2014 02:04:05
Showing 1 changed files
src/gmapR.h
History View file @ f5e63d3
... ... 
@@ -20,11 +20,12 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
20 20 
                 SEXP ignore_query_Ns_p,
21 21 
                 SEXP print_indels_p_R,
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                 SEXP blocksize_R,
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-                SEXP verbosep_R, SEXP max_softclip_R, SEXP noncovered_R);
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+                SEXP verbosep_R, SEXP max_softclip_R, SEXP print_xs_scores_p_R,
24 
+                SEXP noncovered_R);
24 25
25 26 
 SEXP
26 27 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
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-                  SEXP high_base_quality, SEXP which_R);
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+                  SEXP high_base_quality, SEXP which_R, SEXP xs_R);
28 29
29 30 
 SEXP
30 31 
 R_Genome_getSeq (SEXP genome_dir_R, SEXP db_R,
Browse code

add support for the noncovered argument; tells bam_tally to report even those positions that have no coverage

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89724 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 30/04/2014 17:05:27
Showing 1 changed files
src/gmapR.h
History View file @ 6d5d75f
... ... 
@@ -20,7 +20,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
20 20 
                 SEXP ignore_query_Ns_p,
21 21 
                 SEXP print_indels_p_R,
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                 SEXP blocksize_R,
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-                SEXP verbosep_R, SEXP max_softclip_R);
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+                SEXP verbosep_R, SEXP max_softclip_R, SEXP noncovered_R);
24 24
25 25 
 SEXP
26 26 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
Browse code

update GSTRUCT (bam_tally); add include_soft_clip parameter for counting over soft clips of a given max length (more accurate allele frequency)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88343 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/04/2014 22:03:40
Showing 1 changed files
src/gmapR.h
History View file @ 17db5e7
... ... 
@@ -20,7 +20,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
20 20 
                 SEXP ignore_query_Ns_p,
21 21 
                 SEXP print_indels_p_R,
22 22 
                 SEXP blocksize_R,
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-                SEXP verbosep_R);
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+                SEXP verbosep_R, SEXP max_softclip_R);
24 24
25 25 
 SEXP
26 26 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
Browse code

update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80611 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 20/09/2013 02:05:42
Showing 1 changed files
src/gmapR.h
History View file @ 4d5cc80
... ... 
@@ -10,7 +10,7 @@ R_Bamread_new (SEXP bamfile_R);
10 10
11 11 
 SEXP
12 12 
 R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
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-                SEXP which_R,
13 
+                SEXP which_R, SEXP desired_read_group_R,
14 14 
                 SEXP alloclength_R,
15 15 
                 SEXP minimum_mapq_R, SEXP good_unique_mapq_R,
16 16 
                 SEXP maximum_nhits_R,
Browse code

Add R_Genome_getSeq for efficiently retrieving sequence from a GMAP genome index. This is super fast.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@74871 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/03/2013 21:38:39
Showing 1 changed files
src/gmapR.h
History View file @ 86afb16
... ... 
@@ -15,7 +15,7 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
15 15 
                 SEXP minimum_mapq_R, SEXP good_unique_mapq_R,
16 16 
                 SEXP maximum_nhits_R,
17 17 
                 SEXP need_concordant_p_R, SEXP need_unique_p_R,
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-                SEXP need_primary_p_R,
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+                SEXP need_primary_p_R, SEXP ignore_duplicates_p_R,
19 19 
                 SEXP min_depth_R, SEXP variant_strands_R,
20 20 
                 SEXP ignore_query_Ns_p,
21 21 
                 SEXP print_indels_p_R,
... ... 
@@ -26,4 +26,8 @@ SEXP
26 26 
 R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
27 27 
                   SEXP high_base_quality, SEXP which_R);
28 28
29 
+SEXP
30 
+R_Genome_getSeq (SEXP genome_dir_R, SEXP db_R,
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+                 SEXP seqnames_R, SEXP start_R, SEXP width_R, SEXP strand_R);
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+
29 33 
 #endif
Browse code

Decoupling the bam tallying from summarization. Soon, we will return an IIT, which can be summarized in various ways. Currently, the only way is the variant summary.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69806 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 25/09/2012 16:00:17
Showing 1 changed files
src/gmapR.h
History View file @ 3f89995
... ... 
@@ -3,13 +3,14 @@
3 3
4 4 
 #include <Rinternals.h>
5 5
6 
+/* .Call entry points for the gmapR package */
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+
6 8 
 SEXP
7 9 
 R_Bamread_new (SEXP bamfile_R);
8 10
9 11 
 SEXP
10 12 
 R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
11 13 
                 SEXP which_R,
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-                SEXP cycle_breaks_R, SEXP high_quality_cutoff_R,
13 14 
                 SEXP alloclength_R,
14 15 
                 SEXP minimum_mapq_R, SEXP good_unique_mapq_R,
15 16 
                 SEXP maximum_nhits_R,
... ... 
@@ -21,4 +22,8 @@ R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
21 22 
                 SEXP blocksize_R,
22 23 
                 SEXP verbosep_R);
23 24
25 
+SEXP
26 
+R_tally_iit_parse(SEXP tally_iit_R, SEXP cycle_breaks_R,
27 
+                  SEXP high_base_quality, SEXP which_R);
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+
24 29 
 #endif
Browse code

renaming gmapR2 to gmapR: it lives again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2012 22:24:24
Showing 1 changed files
src/gmapR.h
History View file @ b22faf0
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,24 @@
1 
+#ifndef GMAPR_H
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+#define GMAPR_H
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+
4 
+#include <Rinternals.h>
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+
6 
+SEXP
7 
+R_Bamread_new (SEXP bamfile_R);
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+
9 
+SEXP
10 
+R_Bamtally_iit (SEXP bamreader_R, SEXP genome_dir_R, SEXP db_R,
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+                SEXP which_R,
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+                SEXP cycle_breaks_R, SEXP high_quality_cutoff_R,
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+                SEXP alloclength_R,
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+                SEXP minimum_mapq_R, SEXP good_unique_mapq_R,
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+                SEXP maximum_nhits_R,
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+                SEXP need_concordant_p_R, SEXP need_unique_p_R,
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+                SEXP need_primary_p_R,
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+                SEXP min_depth_R, SEXP variant_strands_R,
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+                SEXP ignore_query_Ns_p,
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+                SEXP print_indels_p_R,
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+                SEXP blocksize_R,
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+                SEXP verbosep_R);
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+
24 
+#endif