Merge pull request #18 from 4dn-dcic/dev

Dev

Author: SooLee

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Rpairix
 Title: Rpairix
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: person("Soo", "Lee", email = "duplexa@gmail.com", role = c("aut", "cre"))
 Description: R binder for pairix, tool for querying a pair of genomic ranges in a pairs file (pairix-indexed bgzipped text file)
 Depends:

README.md

@@ -51,7 +51,7 @@ R --no-site-file --no-environ --no-save --no-restore CMD INSTALL --install-tests
 To install a specific version,
 ```r
 library(devtools)
-install_url("https://github.com/4dn-dcic/Rpairix/archive/0.1.2.zip")
+install_url("https://github.com/4dn-dcic/Rpairix/archive/0.1.3.zip")
 ```
 
 
@@ -272,6 +272,9 @@ Individual R functions are written and documented in `R/`. The `src/rpairixlib.c
 ***
 
 ## Version history
+### 0.1.3
+* `px_query`: fixed a new problem (since 0.1.2) with multi-query returning only the last query result.
+
 ### 0.1.2
 * Function `px_get_column_names` is now added.
 * `px_query` now adds column names for the query result if indexing was done with `pairs` preset.

Rpairix.Rproj

@@ -1,4 +1,4 @@
-Version: 0.1.2
+Version: 0.1.3
 
 RestoreWorkspace: No
 SaveWorkspace: No

src/rpairixlib.c

@@ -296,11 +296,11 @@ SEXP get_lines(SEXP _r_pfn, SEXP _r_pquerystr, SEXP _r_pnquery, SEXP _r_pn){
    SEXP _r_presultstr_line[*pn];
    if(tb){
      const ti_conf_t *pconf = ti_get_conf(tb->idx);
-     int i, ires=0;  // i is index for querystr, ires is index for result line
+     int i, ires=0, k=0;  // i is index for querystr, ires is index for result line
      for(i=0;i<*pnquery;i++){
        ti_iter_t iter = ti_querys_2d(tb, pquerystr[i]);
        char *s;
-       int len=-1,k=0;
+       int len=-1;
        while ((s = ti_read(tb, iter, &len)) != 0) {
          int j,start=0,m=0; // j is position on result line, start is start position of the current column, m is the index of the current column
          if(ncols==0) for(j=0;j<=len;j++) if(s[j]==pconf->delimiter||s[j]==0) ncols++;