Hi, I'm running maq2sam-long and it seems to be eating the first N letters of my reads which is a big pain as I'm trying to compare mapping quality between different algorithms to map a solexa run. Any ideas or patches available?
All read id's should start with MID10
ID10_6:1:11989:5823:TGACCA_1_M76-97 16 chr10...
D10_6:1:11988:14238:TGACCA_1_M72-97 16 chr1...
ID10_6:1:11980:7951:TGACCA_1_M76-97 16 chr6...
ID11_6:1:1198:12269:ACAGTG_1_M24-43 0 chr18...
6:1:1198:12269:ACAGTG_2_M0-42_M0-18 16 chr7...
ID12_6:1:11989:4489:GCCAAT_2_M80-97 0 chr2...
MID12_6:1:11982:3900:GCCAAT_2 16 chr13...
MID13_6:1:11982:9036:CAGATC_1 0 chr10...
All read id's should start with MID10
ID10_6:1:11989:5823:TGACCA_1_M76-97 16 chr10...
D10_6:1:11988:14238:TGACCA_1_M72-97 16 chr1...
ID10_6:1:11980:7951:TGACCA_1_M76-97 16 chr6...
ID11_6:1:1198:12269:ACAGTG_1_M24-43 0 chr18...
6:1:1198:12269:ACAGTG_2_M0-42_M0-18 16 chr7...
ID12_6:1:11989:4489:GCCAAT_2_M80-97 0 chr2...
MID12_6:1:11982:3900:GCCAAT_2 16 chr13...
MID13_6:1:11982:9036:CAGATC_1 0 chr10...
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