[med-svn] [Git][med-team/gmap][upstream] New upstream version 2020-11-20+ds
Nilesh Patra
gitlab at salsa.debian.org
Tue Nov 24 16:36:06 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / gmap
Commits:
f262b91c by Nilesh Patra at 2020-11-24T21:54:57+05:30
New upstream version 2020-11-20+ds
- - - - -
6 changed files:
- ChangeLog
- VERSION
- src/get-genome.c
- src/gmap.c
- src/inbuffer.c
- src/inbuffer.h
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,17 @@
+2020-11-20 twu
+
+ * index.html: Updated for latest version
+
+ * VERSION: Updated version number
+
+ * get-genome.c: Added option --transcriptdb to get-genome to retrieve a gene
+ structure
+
+ * gmap.c: Using new interface to Inbuffer_setup
+
+ * inbuffer.c, inbuffer.h: Providing NULL as arguments for genome and
+ genomealt to Request_new
+
2020-11-15 twu
* substring.c: Checking that pos5 < pos3 before Substring trim procedures
=====================================
VERSION
=====================================
@@ -1 +1 @@
-2020-11-14
\ No newline at end of file
+2020-11-20
\ No newline at end of file
=====================================
src/get-genome.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: get-genome.c 223511 2020-11-14 15:50:08Z twu $";
+static char rcsid[] = "$Id: get-genome.c 223600 2020-11-21 04:21:32Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -53,6 +53,8 @@ static bool coordp = false;
static char *genomesubdir = NULL;
static char *dbroot = NULL;
static char *dbversion = NULL;
+static char *transcriptome_dbroot = NULL;
+
static char *user_typestring = NULL;
static int wraplength = 60;
static char *header = NULL;
@@ -90,6 +92,7 @@ static struct option long_options[] = {
/* Input options */
{"dir", required_argument, 0, 'D'}, /* user_genomedir */
{"db", required_argument, 0, 'd'}, /* dbroot */
+ {"transcriptdb", required_argument, 0, 'c'}, /* transcriptome_dbroot */
{"genes", no_argument, 0, 0}, /* genes_file_p */
/* Output options */
@@ -160,10 +163,12 @@ Input options\n\
-D, --dir=STRING Genome directory\n\
-d, --db=STRING Genome database. If argument is '?' (with\n\
the quotes), this command lists available databases.\n\
+ -c, --transcriptdb=STRING\n\
+ Retrieve the gene structure of the given contig argument\n\
+ (Assumes transcriptome was built with gmap_build -c)\n\
--genes Argument is a genes file\n\
\n\
Output options\n\
- -2, --dibase Use dibase version of genome\n\
-C, --coords Show coordinates only\n\
-U, --uppercase Convert sequence to uppercase\n\
-l, --wraplength=INT Wrap length for sequence (default=60)\n\
@@ -953,7 +958,7 @@ main (int argc, char *argv[]) {
int long_option_index = 0;
const char *long_name;
- while ((opt = getopt_long(argc,argv,"D:d:CUl:h:V:v:f:M:m:kru:ESALI^?",
+ while ((opt = getopt_long(argc,argv,"D:d:c:CUl:h:V:v:f:M:m:kru:ESALI^?",
long_options,&long_option_index)) != -1) {
switch (opt) {
case 0:
@@ -1011,6 +1016,7 @@ main (int argc, char *argv[]) {
dbroot = (char *) CALLOC(strlen(optarg)+1,sizeof(char));
strcpy(dbroot,optarg);
break;
+ case 'c': transcriptome_dbroot = optarg; break;
case 'C': coordp = true; break;
case 'U': uppercasep = true; break;
@@ -1051,6 +1057,33 @@ main (int argc, char *argv[]) {
genomesubdir = Datadir_find_genomesubdir(&fileroot,&dbversion,user_genomedir,dbroot);
}
+ if (transcriptome_dbroot != NULL) {
+ iitfile = (char *) MALLOC((strlen(genomesubdir)+strlen("/")+
+ strlen(fileroot)+strlen(".transcripts/")+
+ strlen(transcriptome_dbroot)+strlen(".align.iit")+1)*sizeof(char));
+ sprintf(iitfile,"%s/%s.transcripts/%s.align.iit",genomesubdir,fileroot,
+ transcriptome_dbroot);
+ if ((map_iit = IIT_read(iitfile,/*name*/NULL,true,/*divread*/READ_ALL,/*divstring*/NULL,
+ /*add_iit_p*/true)) == NULL) {
+ fprintf(stderr,"Cannot open IIT file %s\n",iitfile);
+ exit(9);
+ } else if ((index = IIT_find_one(map_iit,argv[0])) < 0) {
+ fprintf(stderr,"Cannot find %s in map file %s\n",argv[0],iitfile);
+ } else {
+ annotation = IIT_annotation(&restofheader,map_iit,index,&allocp);
+ printf("%s",annotation);
+ if (allocp == true) {
+ FREE(restofheader);
+ }
+ }
+
+ IIT_free(&map_iit);
+ FREE(iitfile);
+
+ return 0;
+ }
+
+
if (user_snpsdir == NULL) {
snpsdir = genomesubdir;
} else {
=====================================
src/gmap.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: gmap.c 223529 2020-11-15 02:34:45Z twu $";
+static char rcsid[] = "$Id: gmap.c 223599 2020-11-21 04:19:47Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -6508,7 +6508,7 @@ main (int argc, char *argv[]) {
map_iit,map_divint_crosstable,map_exons_p,map_bothstrands_p,
nflanking,print_comment_p,sam_read_group_id);
- Inbuffer_setup(/*filter_if_both_p*/false,global_genome,global_genomealt);
+ Inbuffer_setup(/*filter_if_both_p*/false);
Outbuffer_setup(argc,argv,optind,chromosome_iit,any_circular_p,
nworkers,orderedp,quiet_if_excessive_p,
=====================================
src/inbuffer.c
=====================================
@@ -1,4 +1,4 @@
-static char rcsid[] = "$Id: inbuffer.c 223511 2020-11-14 15:50:08Z twu $";
+static char rcsid[] = "$Id: inbuffer.c 223598 2020-11-21 04:19:17Z twu $";
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
@@ -37,18 +37,8 @@ static Genome_T global_genomealt;
void
-Inbuffer_setup (bool filter_if_both_p_in
-#ifndef GSNAP
- , Genome_T genome_in, Genome_T genomealt_in
-#endif
- ) {
+Inbuffer_setup (bool filter_if_both_p_in) {
filter_if_both_p = filter_if_both_p_in;
-
-#ifndef GSNAP
- global_genome = genome_in;
- global_genomealt = genomealt_in;
-#endif
-
return;
}
@@ -308,7 +298,7 @@ fill_buffer (T this) {
Sequence_free(&genomeseq);
} else {
debug(printf("inbuffer creating request %d\n",this->requestid));
- this->buffer[nread++] = Request_new(this->requestid++,global_genome,global_genomealt,queryseq);
+ this->buffer[nread++] = Request_new(this->requestid++,/*genome*/NULL,/*genomealt*/NULL,queryseq);
}
this->inputid++;
}
=====================================
src/inbuffer.h
=====================================
@@ -1,4 +1,4 @@
-/* $Id: inbuffer.h 223511 2020-11-14 15:50:08Z twu $ */
+/* $Id: inbuffer.h 223598 2020-11-21 04:19:17Z twu $ */
#ifndef INBUFFER_INCLUDED
#define INBUFFER_INCLUDED
#ifdef HAVE_CONFIG_H
@@ -30,11 +30,7 @@
typedef struct T *T;
extern void
-Inbuffer_setup (bool filter_if_both_p_in
-#ifndef GSNAP
- , Genome_T genome_in, Genome_T genomealt_in
-#endif
- );
+Inbuffer_setup (bool filter_if_both_p_in);
#ifndef GSNAP
extern T
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b
--
View it on GitLab: https://salsa.debian.org/med-team/gmap/-/commit/f262b91c3454421731c6c3ccfee1a6754aef795b
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