08 August 2014

A GNU-make plug-in for the #Illumina FASTQs.

The latest version of GNU-Make http://www.gnu.org/software/make/ provides many advanced capabilities, including many useful functions. However, it does not contain a complete programming language and so it has limitations. Sometimes these limitations can be overcome through use of the shell function to invoke a separate program, although this can be inefficient. On systems which support dynamically loadable objects, you can write your own extension in any language (which can be compiled into such an object) and load it to provide extended capabilities ( see http://www.gnu.org/software/make/manual/make.html#Loading-Objects )

Building a plug-in for the Illumina FASTQs.

from http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm

Illumina FASTQ files use the following naming scheme:

<sample name>_<barcode sequence>_L<lane (0-padded to 3 digits)>_R<read number>_<set number (0-padded to 3 digits>.fastq.gz

For example, the following is a valid FASTQ file name:


Here I'm writing a set of new functions for makefile to extract the different parts (sample, lane...) of a fastq file-name:

The code is available on github.com at

First a struct holding the parts of the file is created:

enum E_IlluminaComponent

typedef struct illumina_scheme_t
    char* filename;
    char* components[NUM_ILLUMINA_COMPONENTS];
    } IlluminaScheme,*IlluminaSchemePtr ;

and a function parsing the filenames is created:

IlluminaSchemePtr IlluminaSchemeNew(const char* filename)

when the plugin llumina is loaded as a dynamic C library, the method llumina_gmk_setup is called,
and we tell make about the new functions with gmk_add_function(name,callback,min_args,max_args,no_expand_content) :

int illumina_gmk_setup ()
   gmk_add_function ("illumina_sample",illumina_sample, 1, 1, 0);
   gmk_add_function ("illumina_lane",illumina_lane, 1, 1, 0);

A function registered with make must match the gmk_func_ptr type.
It will be invoked with three parameters: name (the name of the function), argc (the number of arguments to the function), and argv (an array of pointers to arguments to the function). The last pointer (that is, argv[argc]) will be null (0).
The return value of the function is the result of expanding the function.

char* illumina_sample(const char *function_name, unsigned int argc, char **argv)
    /** extract the filename(s), build and return a string containing the samples */


the plugin must be compiled as a dynamic C library.

Note: The manual says this step can also be generated in the final 'Makefile' (via load ./illumina.so) but I was not able to compile a missing library (illumina.so cannot open shared object file: No such file or directory)

so I compiled it by hand:

gcc -Wall -I/path/to/sources/make-4.0 -shared -fPIC -o illumina.so illumina.c


here is the makefile:

SAMPLES=  NA10831_ATCACG_L002_R1_001.fastq.gz \
      hello \
      NA10832_ATCACG_L002_R1_001.fastq.gz \
      NA10831_ATCACG_L002_R2_001.fastq.gz \
      NA10832_ATCACG_L002_R2_001.fastq.gz \
      NA10833_ATCAGG_L003_R1_003.fastq.gz \
      NA10833_ATCAGG_L003_R1_003.fastq.gz \
      ERROR_ATCAGG_x003_R3_0z3.fastq.gz \

    @echo "SAMPLES: " $(illumina_sample  ${SAMPLES} )
    @echo "BARCODES: " $(illumina_barcode  ${SAMPLES} )
    @echo "LANE: " $(illumina_lane  ${SAMPLES} )
    @echo "READ: " $(illumina_read  ${SAMPLES} )
    @echo "SET: " $(illumina_set  ${SAMPLES} )


$ make
SAMPLES:  NA10831 NA10832 NA10833
LANE:  L002 L003
READ:  R1 R2
SET:  001 003

That's it,