Add 10x tgz input support with extracting aligned/unaligned reads

[olgabot]

Replaces #47

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[pranathivemuri]

// gzipped files are 20 bytes when "empty" due to the header - on mac they were 58 bytes when I was testing? maybe there should be a better check for seeing if the gzipped file is empty than size?

[pranathivemuri]

maybe something like this - https://unix.stackexchange.com/questions/6758/how-can-i-check-if-a-gzipped-file-is-empty

[olgabot]

// gzipped files are 20 bytes when "empty" due to the header - on mac they were 58 bytes when I was testing? maybe there should be a better check for seeing if the gzipped file is empty than size?

Oh hmm interesting. I was using the -profile docker setting so that's a really good catch for e.g. -profile conda on the local system.

[olgabot]

@pranathivemuri Is this something you could add? A check for empty gzipped files?

[pranathivemuri]

we could check it inside the count_umis.py program if record_count == 0 in that fastq.gz file

    with screed.open(path) as f:
        record_count = 0
        for record in f:
            record_count += 1
    if record_count == 0:
           return 

[olgabot]

Closing in favor of #63