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ngsfilter and ecopcr: now check for primers too long for apat library to

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handle (31bp max) and switch to version 3.0.1b23
This commit is contained in:
Celine Mercier
2023-05-12 17:04:21 +12:00
parent 55b2679b23
commit 1c9a906f5b
3 changed files with 23 additions and 5 deletions
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17
src/obi_ecopcr.c
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@ -18,6 +18,7 @@
#include "libecoPCR/ecoPCR.h"
#include "libecoPCR/libthermo/nnparams.h"
#include "libecoPCR/libapat/apat.h"
#include "obi_ecopcr.h"
#include "obidms.h"
@ -365,8 +366,6 @@ static int print_seq(Obiview_p i_view, Obiview_p o_view,
int32_t i;
// TODO add check for primer longer than MAX_PAT_LEN (32)
// Get sequence id
seq_id = obi_get_str_with_elt_idx_and_col_p_in_view(i_view, i_id_column, i_idx, 0);
@ -751,6 +750,20 @@ int obi_ecopcr(const char* i_dms_name,
o1c = complementPattern(o1);
o2c = complementPattern(o2);
// check for primers equal or longer than MAX_PAT_LEN (32)
if (strlen(primer1) >= MAX_PAT_LEN)
{
obi_set_errno(OBI_ECOPCR_ERROR);
obidebug(1, "\nError: first primer is too long, needs to be < 32bp (%s)", primer1);
return -1;
}
if (strlen(primer2) >= MAX_PAT_LEN)
{
obi_set_errno(OBI_ECOPCR_ERROR);
obidebug(1, "\nError: second primer is too long, needs to be < 32bp (%s)", primer2);
return -1;
}
// Open input DMS
i_dms = obi_open_dms(i_dms_name, false);
if (i_dms == NULL)