obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Added signal catching and handling in C and Cython

Browse Source
This commit is contained in:
Celine Mercier
2019-09-21 16:47:22 +02:00
parent 06f9d6da60
commit ec0737a600
23 changed files with 178 additions and 25 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
src/build_reference_db.c
View File

@ -24,6 +24,7 @@
#include "obidms.h"
#include "obidebug.h"
#include "obierrno.h"
#include "obisig.h"
#include "obitypes.h"
#include "obiview.h"
#include "obi_lcs.h"
@ -171,6 +172,8 @@ int build_reference_db(const char* dms_name,
char threshold_str[5];
char* new_comments;
signal(SIGINT, sig_handler);
// Discuss keeping the matrix view or not
matrix_view_name = calloc((strlen(o_view_name)+strlen("_matrix")+1), sizeof(char));
if (matrix_view_name == NULL)
@ -321,6 +324,9 @@ int build_reference_db(const char* dms_name,
// For each pair
for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++)
{
if (! keep_running)
return -1;
// Read all taxids associated with the first sequence and compute their LCA
// Read line index
idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
@ -440,6 +446,9 @@ int build_reference_db(const char* dms_name,
// Going through matrix once, filling refs arrays on the go for efficiency
for (i=0; i<(matrix_with_lca_view->infos)->line_count; i++)
{
if (! keep_running)
return -1;
// Read ref line indexes
idx1 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx1_column, i, 0);
idx2 = obi_get_int_with_elt_idx_and_col_p_in_view(matrix_with_lca_view, matrix_idx2_column, i, 0);