I'm re-posting this to bug visible from the BTS. On 09/06/2017 10:13, Dejan Latinovic wrote:
There were the patch for this issue in earlier bowtie version: https://sources.debian.net/src/bowtie/1.1.2-6/debian/patches/no_hash_style_both_for_mips.patch/ This patch prevents using hash style both for mips, in 1.2.0 version it is empty for some reason.
Indeed, it was reverted in R23797: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/bowtie/trunk/debian/patches/no_hash_style_both_for_mips.patch?r1=23797&r2=23796&pathrev=23797
