Thank you. I'm in the middle of large run at the moment and won't be
able to say with any certainty yet. But I did eyeball some before and
after results without stumbling over anything obvious. I'll confirm asap.
Aaron Darling wrote:
Nice work Mike!
Does this patch have any effect on the effective search space
calculation? Does mpiblast get the right e-values when using gi lists
with this patch?
-Aaron
Michael Cariaso wrote:
The attached patch allows mpiblast to support the -l switch.
This patch will modify the ncbi_Dec2005_evalue.patch file.
The modified patch will make a one line change to ncbi/tools/blastool.c
It may be advisable to patch a fresh version of the Dec2005 toolbox.
patch -p0 [--dry-run] < mpiblast/ncbi_Dec2005_evalue.patch
Recompile ncbi directory:
ncbi/make/makedis.csh
cd mpiblast
make clean (is necessary)
make
The patch makes the line below conditional on
!options->calculate_statistics_and_exit
In the last installment:
Michael Cariaso wrote:
> I'm starting to suspect that the ncbi patch does not alter a code
path
> related to -l gi filtering.
...
The problem probably occurs here:
>
if (options->gifile) {
------------------------------------------------------------------------
Index: ncbi_Dec2005_evalue.patch
===================================================================
RCS file: /cvsroot/mpiblast/mpiblast/ncbi_Dec2005_evalue.patch,v
retrieving revision 1.1
diff -w -u -r1.1 ncbi_Dec2005_evalue.patch
--- ncbi_Dec2005_evalue.patch 20 Dec 2005 02:23:13 -0000 1.1
+++ ncbi_Dec2005_evalue.patch 8 Jan 2006 01:01:51 -0000
@@ -168,3 +168,15 @@
}
+diff -rwu ncbi/tools/blastool.c ncbi.better/tools/blastool.c
+--- ncbi/tools/blastool.c 2005-11-18 09:19:25.000000000 -0500
++++ ncbi.better/tools/blastool.c 2006-01-07 04:11:11.000000000
-0500
+@@ -2792,7 +2792,7 @@
+ if (gi_list)
+ bglp = CombineDoubleInt4Lists(gi_list, gi_list_size, NULL, 0);
+ +- if (options->gifile) {
++ if (options->gifile && !options->calculate_statistics_and_exit) {
+ + if ((tmp_list = GetGisFromFile(options->gifile, &ngis))) {
+ if (bglp) {
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