Gsnap uses the same flags as every other aligner (i.e., 0x4 means unmapped), there's a specification. Something like the following will convert to fastq:
samtools view -f 0x4 foo.bam | awk 'BEGIN{OFS=""}{print ">",$1,"\n",$10,"\n+\n",$11;}' > foo.unmapped.fastq
Edit: Given your comment, if you want to keep pairs intact, then something like the following will work (it assumes that mates have the same name and are sequential, so don't expect it to work otherwise):
#!/usr/bin/env python
import csv
import sys
if(len(sys.argv) != 2) :
print("Usage: samtools view -f 0x4 foo.bam | %s prefix\n" % sys.argv[0])
sys.exit(1)
f = csv.reader(sys.stdin, dialect="excel-tab")
prefix = sys.argv[1]
paired1 = open("%s_1.fastq" % prefix, "w")
paired2 = open("%s_2.fastq" % prefix, "w")
unpaired = open("%s.unpaired.fastq" % prefix, "w")
last = None
for line in f :
if(last == None) :
last = [line[0], line[9], line[10]]
else :
if(last[0] == line[0]) :
paired1.write("%s\n%s\n+\n%s\n" % (last[0], last[1], last[2]))
paired2.write("%s\n%s\n+\n%s\n" % (line[0], line[9], line[10]))
last = None
else :
unpaired.write("%s\n%s\n+\n%s\n" % (last[0], last[1], last[2]))
last = [line[0], line[9], line[10]]
if(last != None) :
unpaired.write("%s\n%s\n+\n%s\n" % (last[0], last[1], last[2]))
paired1.close()
paired2.close()
unpaired.close()
If you saved that as foo.py and made it executable, then something like samtools view -f 0x4 somefile.bam | ./foo.py blah will produce blah_1.fastq, blah_2.fastq and blah.unpaired.fastq.
