not compiling because of DB_CSS to DB_CCS change

[mcshane]

DB_CSS was changed to DB_CCS in 917f6f1a8986c0e338a468155d2951bc3208e289, but was not updated in dex2DB.c. Does not compile currently.

index 22f965d..76ab8c5 100644
--- a/dex2DB.c
+++ b/dex2DB.c
@@ -647,7 +647,7 @@ int main(int argc, char *argv[])
                 offset += clen;

                 if (pwell == s->well)
-                  { prec[pcnt].flags |= DB_CSS;
+                  { prec[pcnt].flags |= DB_CCS;
                     pcnt += 1;
                     if (pcnt >= pmax)
                       { pmax = ((int) (pcnt*1.2)) + 100;
@@ -843,7 +843,7 @@ int main(int argc, char *argv[])
                 offset += clen;

                 if (pwell == rec->well)
-                  { prec[pcnt].flags |= DB_CSS;
+                  { prec[pcnt].flags |= DB_CCS;
                     pcnt += 1;
                     if (pcnt >= pmax)
                       { pmax = ((int) (pcnt*1.2)) + 100;

[thegenemyers]

So sorry. Fixed and checked in.

Shane this is the old version of the scrubber that caused breaks in micro-satellitic regions due to excessive error rates. It is also designed for long subreads and not HiFi reads which makes quite a difference. I do have improved versions for both cases but never took either to the finish line and made them available. I could get one or the other of these two to the point of usability by a third party with a week's work. I offered this before but never got sufficient specifications of what you wanted to proceed. I'd be willing to do this if it is important to you (i.e. you are still trying to fix the missed adaptamer subreads that were discussed the last time I was at Hinxton. I know you like to just get on and often go it alone, but I offer to try connecting on this again if your willing.

 Best,  Gene

On 7/25/20, 11:14 PM, Shane McCarthy wrote:

|DB_CSS| was changed to |DB_CCS| in 917f6f1 https://github.com/thegenemyers/DEXTRACTOR/commit/917f6f1a8986c0e338a468155d2951bc3208e289, but was not updated in |dex2DB.c|. Does not compile currently.

index 22f965d..76ab8c5 100644 --- a/dex2DB.c +++ b/dex2DB.c @@ -647,7 +647,7 @@ int main(int argc, char *argv[]) offset += clen;

              if (pwell == s->well)

• { prec[pcnt].flags |= DB_CSS;

• { prec[pcnt].flags |= DB_CCS; pcnt += 1; if (pcnt >= pmax) { pmax = ((int) (pcnt1.2)) + 100; @@ -843,7 +843,7 @@ int main(int argc, char argv[]) offset += clen;

            if (pwell == rec->well)

• { prec[pcnt].flags |= DB_CSS;
• { prec[pcnt].flags |= DB_CCS; pcnt += 1; if (pcnt >= pmax) { pmax = ((int) (pcnt*1.2)) + 100;

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[mcshane]

Thanks @thegenemyers. Note DEXTRACTOR here also needs updating with the same fix. Not just in DASCRUBBER.

Sorry, I kind of dropped off with the palindrome adapters thing. Yes, would be good to restart that a work again. Will send an email.

[blaiseli]

I have a related compilation failure with the version cloned from github yesterday:

dex2DB.c: In function ‘main’:
dex2DB.c:650:41: error: ‘DB_CSS’ undeclared (first use in this function); did you mean ‘DB_CCS’?
  650 |                   { prec[pcnt].flags |= DB_CSS;
      |                                         ^~~~~~
      |                                         DB_CCS
dex2DB.c:650:41: note: each undeclared identifier is reported only once for each function it appears in
make: *** [Makefile:36: dex2DB] Error 1

As a side note, on my debian-based linux, I had to patch the Makefile so that hdf5 is correctly found. I added the following two variables:

PATH_HDF5_INCLUDE = /usr/include/hdf5/serial
PATH_HDF5_LIB = /usr/lib/x86_64-linux-gnu/hdf5/serial

And then replaced every occurrence of $(PATH_HDF5)/include and $(PATH_HDF5)/lib with $(PATH_HDF5_INCLUDE) and $(PATH_HDF5_LIB) respectively.

[thegenemyers]

Yes, it is DB_CCS. Not sure why such an error is there. -- Gene

On Fri, Jul 8, 2022 at 6:43 AM blaiseli @.***> wrote:

I have a related compilation failure with the version cloned from github yesterday:

dex2DB.c: In function ‘main’:

dex2DB.c:650:41: error: ‘DB_CSS’ undeclared (first use in this function); did you mean ‘DB_CCS’?

650 | { prec[pcnt].flags |= DB_CSS;

  |                                         ^~~~~~

  |                                         DB_CCS

dex2DB.c:650:41: note: each undeclared identifier is reported only once for each function it appears in

make: *** [Makefile:36: dex2DB] Error 1

As a side note, on my debian-based linux, I had to patch the Makefile so that hdf5 is correctly found. I added the following two variables:

PATH_HDF5_INCLUDE = /usr/include/hdf5/serial

PATH_HDF5_LIB = /usr/lib/x86_64-linux-gnu/hdf5/serial

And then replaced every occurrence of $(PATH_HDF5)/include and $(PATH_HDF5)/lib with $(PATH_HDF5_INCLUDE) and $(PATH_HDF5_LIB) respectively.

— Reply to this email directly, view it on GitHub https://github.com/thegenemyers/DEXTRACTOR/issues/26#issuecomment-1178543983, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABUSINW2CS7RJRGJD6FB3V3VS6WX7ANCNFSM4PHUOOTQ . You are receiving this because you were mentioned.Message ID: @.***>