Changeset: b40553856fac for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=b40553856fac
Modified Files:
clients/mapiclient/mclient.c
sql/backends/monet5/bamloader/bam_db_interface.c
sql/backends/monet5/bamloader/bam_db_interface.h
sql/backends/monet5/bamloader/bam_loader.c
sql/backends/monet5/bamloader/bam_wrapper.c
Branch: bamloader
Log Message:
dded SAMrenderer to mclient. Some minor changes in bam loader code.
diffs (230 lines):
diff --git a/clients/mapiclient/mclient.c b/clients/mapiclient/mclient.c
--- a/clients/mapiclient/mclient.c
+++ b/clients/mapiclient/mclient.c
@@ -75,6 +75,12 @@
#endif
#endif
+/* Samtools is not needed for the SAMrenderer, so commented out
+#ifdef HAVE_SAMTOOLS
+#include "bam.h"
+#endif
+*/
+
#ifndef S_ISCHR
#define S_ISCHR(m) (((m) & S_IFMT) == S_IFCHR)
#endif
@@ -116,7 +122,8 @@ enum formatters {
XMLformatter,
TESTformatter,
CLEANformatter,
- TIMERformatter
+ TIMERformatter,
+ SAMformatter
};
static enum formatters formatter = NOformatter;
char *output = NULL; /* output format as string */
@@ -1030,6 +1037,79 @@ TIMERrenderer(MapiHdl hdl)
printf("%s\n", timerHuman());
}
+
+static void
+SAMrenderer(MapiHdl hdl)
+{
+ /* Variables keeping track of which result set fields map to qname, flag
etc. (-1 means that it does not occur in result set) */
+ int field_qname = -1;
+ int field_flag = -1;
+ int field_rname = -1;
+ int field_pos = -1;
+ int field_mapq = -1;
+ int field_cigar = -1;
+ int field_rnext = -1;
+ int field_pnext = -1;
+ int field_tlen = -1;
+ int field_seq = -1;
+ int field_qual = -1;
+
+ int field_count = mapi_get_field_count(hdl);
+ int t_fields;
+
+ int i;
+
+/* Samtools is not needed for rendering to SAM, so this is commented out
+#ifndef HAVE_SAMTOOLS
+ mnstr_printf(toConsole, "Result set can not be rendered to BAM file, since
Samtools could not be found during compilation of mclient\n");
+ return;
+#endif
+*/
+
+ /* First, initialize field variables properly */
+ for(i=0; i<field_count; ++i) {
+ char *field_name = mapi_get_name(hdl, i);
+ if(strcmp(field_name, "qname") == 0) { field_qname = i; continue; }
+ if(strcmp(field_name, "flag" ) == 0) { field_flag = i; continue; }
+ if(strcmp(field_name, "rname") == 0) { field_rname = i; continue; }
+ if(strcmp(field_name, "pos" ) == 0) { field_pos = i; continue; }
+ if(strcmp(field_name, "mapq" ) == 0) { field_mapq = i; continue; }
+ if(strcmp(field_name, "cigar") == 0) { field_cigar = i; continue; }
+ if(strcmp(field_name, "rnext") == 0) { field_rnext = i; continue; }
+ if(strcmp(field_name, "pnext") == 0) { field_pnext = i; continue; }
+ if(strcmp(field_name, "tlen" ) == 0) { field_tlen = i; continue; }
+ if(strcmp(field_name, "seq" ) == 0) { field_seq = i; continue; }
+ if(strcmp(field_name, "qual" ) == 0) { field_qual = i; continue; }
+
+ mnstr_printf(stderr_stream, "Unexpected column name in result set:
'%s'. Data in this column is not used.\n", field_name);
+ }
+
+ /* Write all alignments */
+ while (!mnstr_errnr(toConsole) && (t_fields = fetch_row(hdl)) != 0) {
+ if (t_fields != field_count) {
+ mnstr_printf(stderr_stream,
+ "invalid tuple received from server, "
+ "got %d columns, expected %d,
ignoring\n", t_fields, field_count);
+ continue;
+ }
+
+ /* Write fields to SAM line */
+ mnstr_printf(toConsole, "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n",
+ (field_qname == -1 ? "*" : mapi_fetch_field(hdl, field_qname)),
+ (field_flag == -1 ? "0" : mapi_fetch_field(hdl, field_flag )),
+ (field_rname == -1 ? "*" : mapi_fetch_field(hdl, field_rname)),
+ (field_pos == -1 ? "0" : mapi_fetch_field(hdl, field_pos )),
+ (field_mapq == -1 ? "255" : mapi_fetch_field(hdl, field_mapq )),
+ (field_cigar == -1 ? "*" : mapi_fetch_field(hdl, field_cigar)),
+ (field_rnext == -1 ? "*" : mapi_fetch_field(hdl, field_rnext)),
+ (field_pnext == -1 ? "0" : mapi_fetch_field(hdl, field_pnext)),
+ (field_tlen == -1 ? "0" : mapi_fetch_field(hdl, field_tlen )),
+ (field_seq == -1 ? "*" : mapi_fetch_field(hdl, field_seq )),
+ (field_qual == -1 ? "*" : mapi_fetch_field(hdl, field_qual)));
+ }
+}
+
+
static void
SQLheader(MapiHdl hdl, int *len, int fields, char more)
{
@@ -1381,7 +1461,9 @@ setFormatter(char *s)
formatter = TESTformatter;
} else if (strcmp(s, "timer") == 0) {
formatter = TIMERformatter;
- } else {
+ } else if (strcmp(s, "sam") == 0) {
+ formatter = SAMformatter;
+ } else {
mnstr_printf(toConsole, "unsupported formatter\n");
}
}
@@ -1599,6 +1681,9 @@ format_result(Mapi mid, MapiHdl hdl, cha
case TIMERformatter:
TIMERrenderer(hdl);
break;
+ case SAMformatter:
+ SAMrenderer(hdl);
+ break;
default:
RAWrenderer(hdl);
break;
@@ -1811,7 +1896,7 @@ showCommands(void)
mnstr_printf(toConsole, "\\a - disable auto commit\n");
}
mnstr_printf(toConsole, "\\e - echo the query in sql formatting
mode\n");
- mnstr_printf(toConsole, "\\f - format using a built-in renderer
{csv,tab,raw,sql,xml}\n");
+ mnstr_printf(toConsole, "\\f - format using a built-in renderer
{csv,tab,raw,sql,xml,sam}\n");
mnstr_printf(toConsole, "\\w# - set maximal page width
(-1=unlimited, 0=terminal width, >0=limit to num)\n");
mnstr_printf(toConsole, "\\r# - set maximum rows per page
(-1=raw)\n");
mnstr_printf(toConsole, "\\L file - save client/server interaction\n");
diff --git a/sql/backends/monet5/bamloader/bam_db_interface.c
b/sql/backends/monet5/bamloader/bam_db_interface.c
--- a/sql/backends/monet5/bamloader/bam_db_interface.c
+++ b/sql/backends/monet5/bamloader/bam_db_interface.c
@@ -188,9 +188,6 @@ char buf_sql_copy_into[BUF_SIZE_COPY_INT
-
-/* TODO Find out if executed SQL queries get logged somewhere else already,
since in that case we shouldn't log it again */
-
str
create_schema_if_not_exists(Client cntxt, mvc *m, str schemaname, str descr,
sql_schema **ret) {
sql_schema *result;
diff --git a/sql/backends/monet5/bamloader/bam_db_interface.h
b/sql/backends/monet5/bamloader/bam_db_interface.h
--- a/sql/backends/monet5/bamloader/bam_db_interface.h
+++ b/sql/backends/monet5/bamloader/bam_db_interface.h
@@ -78,5 +78,4 @@ str create_alignment_storage_1(Client cn
str copy_into_db(Client cntxt, bam_wrapper *bw);
str drop_file(Client cntxt, str descr, lng file_id, sht dbschema);
-/* TODO Consider creating something that truncates everything from the BAM
schema */
#endif
diff --git a/sql/backends/monet5/bamloader/bam_loader.c
b/sql/backends/monet5/bamloader/bam_loader.c
--- a/sql/backends/monet5/bamloader/bam_loader.c
+++ b/sql/backends/monet5/bamloader/bam_loader.c
@@ -155,8 +155,6 @@ bam_loader(Client cntxt, MalBlkPtr mb, s
if((msg = create_table_if_not_exists(cntxt, m, s, "pg", SQL_CREATE_PG,
"bam.create_pg", NULL)) != MAL_SUCCEED) goto cleanup;
/* Get next file id */
- /* TODO Find out if we can indeed reserve file ids here. This is only
possible if it is impossible for other MAL instructions
- * to get executed in parallel to the bam loader, since then changes could
be made to the files table while we're calculating */
TO_LOG("<bam_loader> Retrieving next file id...");
if((msg = next_file_id(m, files_table, &cur_file_id)) != MAL_SUCCEED) {
goto cleanup;
diff --git a/sql/backends/monet5/bamloader/bam_wrapper.c
b/sql/backends/monet5/bamloader/bam_wrapper.c
--- a/sql/backends/monet5/bamloader/bam_wrapper.c
+++ b/sql/backends/monet5/bamloader/bam_wrapper.c
@@ -51,7 +51,7 @@ bsopen(str filepath) {
* Takes a bam_wrapper and initializes it. Note that in order for the
accompanying clear function to work, the bam_wrapper
* should be initialized to zero before the fields are filled in by the init
function.
*
- * TODO: Right now, binaries will be opened in dbfarm/bam, since that is the
current working directory. Make sure this is OK.
+ * Binaries will be opened in dbfarm/bam, since that is the current working
directory.
*/
str
init_bam_wrapper(bam_wrapper *bw, str file_location, lng file_id, sht
dbschema) {
@@ -862,12 +862,8 @@ process_alignment(bam_wrapper *bw, lng v
}
/* First save the values in the alignment struct that we have to store in
additional variables anyway */
- a_out->flag = a_in->core.flag;
a_out->pos = a_in->core.pos + 1;
- a_out->mapq = a_in->core.qual;
- a_out->pnext = a_in->core.mpos + 1;
- /* TODO Try out if flag and mapq can be removed, since we would expect
being able to directly access the address of something that is stored inside a
struct */
-
+ a_out->pnext = a_in->core.mpos + 1;
/* Construct cigar, seq and qual strings in the buffers provided in a_out
*/
if(a_in->core.n_cigar == 0) {
@@ -910,7 +906,7 @@ process_alignment(bam_wrapper *bw, lng v
++bw->cnt_alignments;
if(!APPEND_LNG(bw->alignments[0], virtual_offset))
WRITE_ERR_PROCESS_ALIGNMENT("virtual_offset");
if(!APPEND_STR(bw->alignments[1], bam1_qname(a_in)))
WRITE_ERR_PROCESS_ALIGNMENT("qname");
- if(!APPEND_SHT(bw->alignments[2], a_out->flag))
WRITE_ERR_PROCESS_ALIGNMENT("flag");
+ if(!APPEND_SHT(bw->alignments[2], a_in->core.flag))
WRITE_ERR_PROCESS_ALIGNMENT("flag");
if(a_in->core.tid < 0) {
if(!APPEND_STR(bw->alignments[3], "*"))
WRITE_ERR_PROCESS_ALIGNMENT("rname");
@@ -919,7 +915,7 @@ process_alignment(bam_wrapper *bw, lng v
}
if(!APPEND_INT(bw->alignments[4], a_out->pos))
WRITE_ERR_PROCESS_ALIGNMENT("pos");
- if(!APPEND_SHT(bw->alignments[5], a_out->mapq))
WRITE_ERR_PROCESS_ALIGNMENT("mapq");
+ if(!APPEND_SHT(bw->alignments[5], a_in->core.qual))
WRITE_ERR_PROCESS_ALIGNMENT("mapq");
if(!APPEND_STR(bw->alignments[6], a_out->cigar))
WRITE_ERR_PROCESS_ALIGNMENT("cigar");
if(a_in->core.mtid < 0) {
@@ -940,13 +936,14 @@ process_alignment(bam_wrapper *bw, lng v
/* Complete the a_out struct */
a_out->virtual_offset = virtual_offset;
strcpy(a_out->qname, bam1_qname(a_in));
+ a_out->flag = a_in->core.flag;
if(a_in->core.tid < 0) {
a_out->rname = "*";
} else {
a_out->rname = bw->header->target_name[a_in->core.tid];
}
-
+ a_out->mapq = a_in->core.qual;
if(a_in->core.mtid < 0) {
a_out->rnext = "*";
} else if(a_in->core.mtid == a_in->core.tid) {
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