 Use read name only to determine if alignment has other things which have been kept during downsampling.
 Use read name only to determine if alignment has other things which have been kept during downsampling.

 This should capture secondary and chimeric alignments, as well as read pairs

IGV-2065

itenente/igv,godotgildor/igv,igvteam/igv,itenente/igv,itenente/igv,igvteam/igv,igvteam/igv,itenente/igv,igvteam/igv,godotgildor/igv,itenente/igv,amwenger/igv,godotgildor/igv,igvteam/igv,amwenger/igv,amwenger/igv,amwenger/igv,amwenger/igv,godotgildor/igv,godotgildor/igv