to-mr produces unexpected files with garbled reads

[vmkalbskopf]

to-mr -o 1455.mr ../1455.srtd.mkdups.rdgrps.bam runs without error. Here are the first 3 lines of the .mr file:

PRELSG_01_v1 119 134 M03562:43:000000000-BLRTF:1:1117:17291:24151 0 - AAGGATCAAAAAGCT PRELSG_01_v1 137 259 FRAG:M03562:43:000000000-BLRTF:1:2111:7502:341 0 - TCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTATTAGTGGGTGAACAATCCAACGCTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACA ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^A^A^A^A<86><FF><FF><FF><E2>4^V=<FE><B8>ȯ<C1>^@^@^@^@^@^@^@<A0><94><E0>a<A4>U^@ ^@^P@<DE>a<A4>U^@^@CATTGTGAAGCAGAATTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTT PRELSG_01_v1 189 259 FRAG:M03562:43:000000000-BLRTF:1:1112:22127:1822 0 - TCATCAGTAGGGTAAAACTAACCTGTCTCACGACGGTCTAAACCCAGCTCACGTTCCCTATTAGTGGGTG ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^A^A^A^A<BA><FF><FF><FF><E5>j&ojX<89>R<C1>^@^@^@^@^@^@^@<A0><94><E0>a<A4>U^@^@^P@<DE>a<A4>U^@^@CATTGTGAAGCAGA

Here are the reads for M03562:43:000000000-BLRTF:1:2111:7502:341 from the bam file:

M03562:43:000000000-BLRTF:1:2111:7502:3413 163 PRELSG_01_v1 138 0 122M59S = 138 122 TGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGATGTGTTGTTGCAATAGTAATCCTGCTCAGTACGAGAGGAACCGCAGGTTCAGACCCCTG CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGGGGCGFGGGGGGFGGGFG7FGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGFGGEFGGGGGGGGGGGGGGGGGGGGGFFGFGGGGGFECEGGGGGGGGEGFEEGGGGGGFG X0:i:4 MD:Z:21G2C6G2T1A3T2C13G64 XE:i:21 PG:Z:MarkDuplicates RG:Z:1 NH:i:4 XI:f:0.9344 NM:i:8 XR:i:122 AS:i:1020 M03562:43:000000000-BLRTF:1:2111:7502:3413 83 PRELSG_01_v1 138 0 122M59S = 138 -122 TGTCGGCTCTTCCTATCATTGTGAAGCAGAATTCACCAAGCGTTGGATTGTTCACCCACTAATAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTGATGATGTGTTGTTGCAATAGTAATCCTGCTCAGTACGAGAGGAACCGCAGGTTCAGACCCCTG GGFGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCCCCC X0:i:4 MD:Z:21G2C6G2T1A3T2C13G64 XE:i:21 PG:Z:MarkDuplicates RG:Z:1 NH:i:4 XI:f:0.9344 NM:i:8 XR:i:122 AS:i:1020

This is RNA seq data.