Not fetching all reads

[cmdcolin]

A small region of a pacbio bam file by samtools contains 34 reads

% node index.jscdiesh-Precision-7540% samtools view https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/m64011_181218_235052.8M.HG002.hs37d5.11kb.bam 1:10000-10600|wc
34 771 777929

By a small script we get less

const fetch = require( 'cross-fetch');

const {RemoteFile} = require('generic-filehandle')
const {BamFile} = require('@gmod/bam')

const b = new BamFile({
>       bamFilehandle: new RemoteFile('https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/m64011_181218_235052.8M.HG002.hs37d5.11kb.bam', {fetch}),
>       baiFilehandle: new RemoteFile('https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/m64011_181218_235052.8M.HG002.hs37d5.11kb.bam.bai', {fetch} )
});

(async () => {
>       await b.getHeader()
>       const ret = await b.getRecordsForRange('1',9999,10600)
>       console.log(ret.length)
})()

//outputs 12

git bisect narrows down squarely to #36

Removing the final vestige of the chunk merging code makes this problem go away for the most part, but actually returns 37 reads instead of 34

https://github.com/GMOD/bam-js/tree/remove_more_chunk_merging

Will need to make it match up to par with what samtools returns

[cmdcolin]

Fixed by #44