diff options
Diffstat (limited to 'sam.h')
| -rw-r--r-- | sam.h | 10 |
1 files changed, 8 insertions, 2 deletions
@@ -1,5 +1,5 @@ /* - * Copyright 2011, Ben Langmead <blangmea@jhsph.edu> + * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu> * * This file is part of Bowtie 2. * @@ -25,6 +25,7 @@ #include "read.h" #include "util.h" #include "aligner_result.h" +#include "scoring.h" enum { // Comments use language from v1.4-r962 spec @@ -70,6 +71,7 @@ public: bool print_as, bool print_xs, bool print_xss, + bool print_yn, bool print_xn, bool print_cs, bool print_cq, @@ -116,6 +118,7 @@ public: print_as_(print_as), // alignment score of best alignment print_xs_(print_xs), // alignment score of second-best alignment print_xss_(print_xss), + print_yn_(print_yn), // minimum valid score and perfect score print_xn_(print_xn), print_cs_(print_cs), print_cq_(print_cq), @@ -286,6 +289,7 @@ public: const AlnSetSumm& summ, // summary of alignments for this read const SeedAlSumm& ssm, // seed alignment summary const PerReadMetrics& prm, // per-read metics + const Scoring& sc, // scoring scheme const char *mapqInp) // inputs to MAPQ calculation const; @@ -299,7 +303,8 @@ public: const AlnFlags& flags, // alignment flags const AlnSetSumm& summ, // summary of alignments for this read const SeedAlSumm& ssm, // seed alignment summary - const PerReadMetrics& prm) // per-read metrics + const PerReadMetrics& prm, // per-read metrics + const Scoring& sc) // scoring scheme const; /** @@ -337,6 +342,7 @@ protected: bool print_as_; // AS:i: Alignment score generated by aligner bool print_xs_; // XS:i: Suboptimal alignment score bool print_xss_;// Xs:i: Best invalid alignment score found + bool print_yn_; // YN:i:, Yn:i: minimum valid score and perfect score bool print_xn_; // XN:i: Number of ambiguous bases in the referenece // Other optional flags |