Commit 0b62619e authored by Celine Mercier's avatar Celine Mercier

Various commentaries and insignificant fixes

parent c7f5b8d9
......@@ -2,6 +2,7 @@
from obitools3.dms.capi.obitypes cimport obitype_t, index_t
cdef obi_errno_to_exception(int obi_errno, index_t line_nb=*, object elt_id=*, str error_message=*)
cdef bytes str2bytes(str string)
......
......@@ -16,9 +16,7 @@ from obitools3.dms.capi.obierrno cimport OBI_LINE_IDX_ERROR, \
#obi_errno
import re
#from obitools3.dms.obiseq cimport Nuc_Seq, Nuc_Seq_Stored
# TODO RollbackException?
cdef obi_errno_to_exception(int obi_errno, index_t line_nb=-1, object elt_id=None, str error_message=None) :
......
......@@ -359,6 +359,8 @@ 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)
ldelta = (pos1 <= keep_nucleotides)?pos1:keep_nucleotides;
rdelta = ((pos2+keep_nucleotides)>=seq_len)?seq_len-pos2:keep_nucleotides;
......
......@@ -1351,8 +1351,9 @@ OBIDMS_column_p obi_open_column(OBIDMS_p dms,
column->writable = false;
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL, the associated indexer is opened
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL))
// If the data type is OBI_STR, OBI_SEQ or OBI_QUAL or the column contains tuples, the associated indexer is opened
// TODO maybe store a 'indexer' bool in the header instead
if (((column->header)->returned_data_type == OBI_STR) || ((column->header)->returned_data_type == OBI_SEQ) || ((column->header)->returned_data_type == OBI_QUAL) || ((column->header)->tuples))
{
column->indexer = obi_open_indexer(dms, (column->header)->indexer_name);
if (column->indexer == NULL)
......
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