1. gmapR
  2. src
  3. R_init_gmapR.c
Browse code

support new version of bam_tally

Michael Lawrence authored on 12/06/2019 22:48:54
Showing 1 changed files
src/R_init_gmapR.c
History View file @ c3db7e3
... ... 
@@ -7,7 +7,7 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
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9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 26),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 28),
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   CALLMETHOD_DEF(R_tally_iit_parse, 6),
12 12
13 13 
   /* bamreader.c */
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/R_init_gmapR.c
History View file @ 685d60e
... ... 
@@ -7,7 +7,7 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 25),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 26),
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   CALLMETHOD_DEF(R_tally_iit_parse, 6),
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13 13 
   /* bamreader.c */
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/R_init_gmapR.c
History View file @ 8418591
... ... 
@@ -7,8 +7,8 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 21),
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-  CALLMETHOD_DEF(R_tally_iit_parse, 5),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 25),
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+  CALLMETHOD_DEF(R_tally_iit_parse, 6),
12 12
13 13 
   /* bamreader.c */
14 14 
   CALLMETHOD_DEF(R_Bamread_new, 1),
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/R_init_gmapR.c
History View file @ d5ed124
... ... 
@@ -7,8 +7,8 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 25),
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-  CALLMETHOD_DEF(R_tally_iit_parse, 6),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 21),
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+  CALLMETHOD_DEF(R_tally_iit_parse, 5),
12 12
13 13 
   /* bamreader.c */
14 14 
   CALLMETHOD_DEF(R_Bamread_new, 1),
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/R_init_gmapR.c
History View file @ c8fd96e
... ... 
@@ -7,8 +7,8 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
10 
-  CALLMETHOD_DEF(R_Bamtally_iit, 21),
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-  CALLMETHOD_DEF(R_tally_iit_parse, 5),
10 
+  CALLMETHOD_DEF(R_Bamtally_iit, 25),
11 
+  CALLMETHOD_DEF(R_tally_iit_parse, 6),
12 12
13 13 
   /* bamreader.c */
14 14 
   CALLMETHOD_DEF(R_Bamread_new, 1),
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/R_init_gmapR.c
History View file @ c78be69
... ... 
@@ -7,8 +7,8 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 22),
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-  CALLMETHOD_DEF(R_tally_iit_parse, 6),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 21),
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+  CALLMETHOD_DEF(R_tally_iit_parse, 5),
12 12
13 13 
   /* bamreader.c */
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   CALLMETHOD_DEF(R_Bamread_new, 1),
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/R_init_gmapR.c
History View file @ f5e63d3
... ... 
@@ -7,8 +7,8 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 21),
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-  CALLMETHOD_DEF(R_tally_iit_parse, 5),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 22),
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+  CALLMETHOD_DEF(R_tally_iit_parse, 6),
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13 13 
   /* bamreader.c */
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   CALLMETHOD_DEF(R_Bamread_new, 1),
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/R_init_gmapR.c
History View file @ 6d5d75f
... ... 
@@ -7,7 +7,7 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 20),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 21),
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   CALLMETHOD_DEF(R_tally_iit_parse, 5),
12 12
13 13 
   /* bamreader.c */
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/R_init_gmapR.c
History View file @ 17db5e7
... ... 
@@ -7,7 +7,7 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
10 
-  CALLMETHOD_DEF(R_Bamtally_iit, 19),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 20),
11 11 
   CALLMETHOD_DEF(R_tally_iit_parse, 5),
12 12
13 13 
   /* bamreader.c */
Browse code

add calculation of median-distance-from-nearest-end to variantSummary()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@86188 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 07/02/2014 01:07:22
Showing 1 changed files
src/R_init_gmapR.c
History View file @ 7c26346
... ... 
@@ -8,7 +8,7 @@ static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
10 10 
   CALLMETHOD_DEF(R_Bamtally_iit, 19),
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-  CALLMETHOD_DEF(R_tally_iit_parse, 4),
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+  CALLMETHOD_DEF(R_tally_iit_parse, 5),
12 12
13 13 
   /* bamreader.c */
14 14 
   CALLMETHOD_DEF(R_Bamread_new, 1),
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/R_init_gmapR.c
History View file @ 4d5cc80
... ... 
@@ -7,7 +7,7 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
10 
-  CALLMETHOD_DEF(R_Bamtally_iit, 18),
10 
+  CALLMETHOD_DEF(R_Bamtally_iit, 19),
11 11 
   CALLMETHOD_DEF(R_tally_iit_parse, 4),
12 12
13 13 
   /* bamreader.c */
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/R_init_gmapR.c
History View file @ 86afb16
... ... 
@@ -7,11 +7,14 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 17),
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+  CALLMETHOD_DEF(R_Bamtally_iit, 18),
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   CALLMETHOD_DEF(R_tally_iit_parse, 4),
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13 13 
   /* bamreader.c */
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   CALLMETHOD_DEF(R_Bamread_new, 1),
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+
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+  /* genome.c */
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+  CALLMETHOD_DEF(R_Genome_getSeq, 6),
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   {NULL, NULL, 0}
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 };
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/R_init_gmapR.c
History View file @ 3f89995
... ... 
@@ -7,8 +7,9 @@
7 7 
 static const R_CallMethodDef callMethods[] = {
8 8
9 9 
   /* bamtally.c */
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-  CALLMETHOD_DEF(R_Bamtally_iit, 19),
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-
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+  CALLMETHOD_DEF(R_Bamtally_iit, 17),
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+  CALLMETHOD_DEF(R_tally_iit_parse, 4),
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+
12 13 
   /* bamreader.c */
13 14 
   CALLMETHOD_DEF(R_Bamread_new, 1),
14 15
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
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src/R_init_gmapR.c
History View file @ b22faf0
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,21 @@
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+#include <R_ext/Rdynload.h>
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+
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+#include "gmapR.h"
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+
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+#define CALLMETHOD_DEF(fun, numArgs) {#fun, (DL_FUNC) &fun, numArgs}
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+
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+static const R_CallMethodDef callMethods[] = {
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+
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+  /* bamtally.c */
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+  CALLMETHOD_DEF(R_Bamtally_iit, 19),
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+
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+  /* bamreader.c */
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+  CALLMETHOD_DEF(R_Bamread_new, 1),
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+
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+  {NULL, NULL, 0}
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+};
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+
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+void R_init_gmapR(DllInfo *info)
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+{
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+  R_registerRoutines(info, NULL, callMethods, NULL, NULL);
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+}