basset_sad throws an error for variants near the chromosome start

[arahuja]

  File "/Users/arahuja/src/Basset/src/basset_sad.py", line 198, in <module>
    main()
  File "/Users/arahuja/src/Basset/src/basset_sad.py", line 54, in main
    seq_vecs, seqs, seq_headers = vcf.snps_seq1(snps, options.genome_fasta, options.seq_len)
  File "/Users/arahuja/src/Basset/src/vcf.py", line 57, in snps_seq1
    seq = genome.fetch(snp.chrom, seq_start-1, seq_end).upper()
  File "pysam/cfaidx.pyx", line 238, in pysam.cfaidx.FastaFile.fetch (pysam/cfaidx.c:3991)
  File "pysam/cutils.pyx", line 202, in pysam.cutils.parse_region (pysam/cutils.c:3378)
ValueError: start out of range (-228)

This is due to an issue in vcf.py where the seq_start is not check to be < 0 when variant start < window size

[davek44]

Thanks for pointing that out. The newest commit should fix it.