I needed the inverse, selecting only spliced reads. Using python, save this as select_spliced_reads.py and execute as python only_spliced_reads.py -b input.bam -o spliced.bam

import pysam
from argparse import ArgumentParser


def main():
    args = get_args()
    get_spliced_reads(args)


def get_args():
    parser = ArgumentParser("")
    parser.add_argument("-b", "--bam", help="input bam", required=True)
    parser.add_argument("-o", "--output", help="output bam", required=True)
    parser.add_argument("-i", "--introns", help="minimal number of introns", default=1, type=int)
    return parser.parse_args()


def get_spliced_reads(args):
    bam_file = pysam.AlignmentFile(args.bam, "rb")
    out_file = pysam.AlignmentFile(args.output, "wb", template=bam_file)
    for read in bam_file.fetch():
        if sum(operation == 3 for (operation, _) in read.cigartuples) > args.introns:
            out_file.write(read)
    bam_file.close()
    out_file.close()


if __name__ == "__main__":
    main()

Using picard FilterSamReads http://broadinstitute.github.io/picard/command-line-overview.html#Overview and a javascript filter (not tested)

java -jar picard.jar FilterSamReads \
       I=input.bam \ 
       O=output.bam \
      JAVASCRIPT_FILE=filter.js

with filter.js

function accept(r) {
if(r.getReadUnmappedFlag()) return true;
var i,c= r.getCigar();
if(c==null) return true;
for( i=0;i< c. numCigarElements() ;++i) {
  if(  c. getCigarElement(i).getOperator().name().equals("N") ) return false;
  }
return true;
}

accept(record);

Using the BBMap package:

reformat.sh in=mapped.bam out=filtered.bam maxdellen=50

You can set "maxdellen" to whatever length deletion event you consider the minimum to signify splicing, which depends on the organism.