bam/sam.h

[simonkidd]

Hi

After a successful ./configure I run make I get an fatal error that reads:

make[1]: Entering directory `.../shendurelab-LACHESIS-2e27abb/src/include/gtools'
g++ -c SAMStepper.cc -Wall -ansi -pedantic -g -O3 -std=c++11 
In file included from SAMStepper.cc:18:0:
**SAMStepper.h:65:21: fatal error: bam/sam.h: No such file or directory**
 **#include <bam/sam.h>**
                     ^
compilation terminated.
make[1]: *** [SAMStepper.o] Error 1

I tried to get around the issue by creating a symbolic link back into samtools to where sam.h is within 'src/include/gtools/' (creating the bam folder 'src/include/gtools/bam/') but it still fails to read the file.

Any help would be really appreciated.

Thanks,
Simon

[pkubgmlixs]

Hi,
I got the same fatal error, too. And have you solved this error?

[simonkidd]

Sorry pkubgmlixs, I haven't had any responses andhaven't revisited it myself but will soon and post any update should I have any.

Thanks.

[GitHub-Lujianjun]

Hi guys：
While this error appeared，means that your need to update gcc and g++.
BTW, gcc-4.8.2 is necessary.
Good luck!
JJLu

[WTarabidopsis]

Hi guys：
While this error appeared，means that your need to update gcc and g++.
BTW, gcc-4.8.2 is necessary.
Good luck!
JJLu

Hi JJ,
I also encountered the same problem with gcc version 4.8.5, any other solutions?
Thanks!

[mehmetdayi]

Hi
Did you solve it?
I am having the same issue.

[mehmetdayi]

I solved and am adding solution here in case someone alse may need.

First you need to edit SAMStepper.h and SAMStepper.cc files in /src/include/gtools directory by adding the directory after -I flag and a bam.h file after #include line.

For instance (SAMStepper.h file editing);

// To compile using this, you must include -I /home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian
#include "/home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian/sam.h"

You should do the same editing for SAMStepper.cc.

Then you can run make and later make install.

[RanSenn]

I solved and am adding solution here in case someone alse may need.

First you need to edit SAMStepper.h and SAMStepper.cc files in /src/include/gtools directory by adding the directory after -I flag and a bam.h file after #include line.

For instance (SAMStepper.h file editing);

// To compile using this, you must include -I /home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian #include "/home/user10/applications/LACHESIS/samtools-legacy_0.1.19_debian/sam.h"

You should do the same editing for SAMStepper.cc.

Then you can run make and later make install.

It works！Thank You Very Much！