diff --git a/src/call_genotypes.rs b/src/call_genotypes.rs
index cb03950..6e6ea74 100644
--- a/src/call_genotypes.rs
+++ b/src/call_genotypes.rs
@@ -197,7 +197,7 @@ pub fn call_genotypes_no_haplotypes(
             &var.alleles,
             max_p_miscall,
         )
-            .chain_err(|| "Error calculating genotype posteriors for haplotype-free genotyping")?;
+        .chain_err(|| "Error calculating genotype posteriors for haplotype-free genotyping")?;
 
         // get the genotype with maximum genotype posterior
         let (max_g, max_post) = posts.max_genotype_post(false, false);
@@ -415,7 +415,8 @@ pub fn call_genotypes_with_haplotypes(
             if var.alleles.len() == 2
                 && (var.genotype == Genotype(0, 1) || var.genotype == Genotype(1, 0))
                 && var.alleles[0].len() == 1
-                && var.alleles[1].len() == 1 {
+                && var.alleles[1].len() == 1
+            {
                 var_phased[i] = true;
 
                 if var.genotype == Genotype(0, 1) {
@@ -597,8 +598,10 @@ pub fn call_genotypes_with_haplotypes(
                         }
 
                         // get the value of the read likelihood given each haplotype
-                        let (mut p_read_h0, mut p_read_h1) = (p_read_hap[0][call.frag_ix as usize],
-                                                              p_read_hap[1][call.frag_ix as usize]);
+                        let (mut p_read_h0, mut p_read_h1) = (
+                            p_read_hap[0][call.frag_ix as usize],
+                            p_read_hap[1][call.frag_ix as usize],
+                        );
 
                         if var_phased[v as usize] {
                             // for each haplotype allele
@@ -677,10 +680,10 @@ pub fn call_genotypes_with_haplotypes(
                     if var_phased[v as usize] {
                         for &(frag_ix, p_read_h0, p_read_h1) in
                             &p_read_lst_genotype[max_g.0 as usize][max_g.1 as usize]
-                            {
-                                p_read_hap[0][frag_ix] = p_read_h0;
-                                p_read_hap[1][frag_ix] = p_read_h1;
-                            }
+                        {
+                            p_read_hap[0][frag_ix] = p_read_h0;
+                            p_read_hap[1][frag_ix] = p_read_h1;
+                        }
                     }
                 }
 
@@ -790,7 +793,7 @@ pub fn call_genotypes_with_haplotypes(
             "{}.{}.haplotype_genotype_iteration.vcf",
             program_step, hapcut2_iter
         )
-            .to_owned();
+        .to_owned();
         print_variant_debug(
             varlist,
             &interval,
@@ -826,11 +829,11 @@ mod tests {
     fn test_generate_fragcall_pileup() {
         let fcall = |f_ix, v_ix, a| {
             FragCall {
-                frag_ix: f_ix,                       // index into fragment list
-                var_ix: v_ix,                              // index into variant list
-                allele: a,                                 // allele call
+                frag_ix: f_ix,                   // index into fragment list
+                var_ix: v_ix,                    // index into variant list
+                allele: a,                       // allele call
                 qual: LogProb::from(Prob(0.01)), // LogProb probability the call is an error
-                one_minus_qual: LogProb::from(Prob(0.99))
+                one_minus_qual: LogProb::from(Prob(0.99)),
             }
         };
         let p50 = LogProb::from(Prob(0.5));
diff --git a/src/call_potential_snvs.rs b/src/call_potential_snvs.rs
index ab1e98c..ad74fc3 100644
--- a/src/call_potential_snvs.rs
+++ b/src/call_potential_snvs.rs
@@ -257,7 +257,7 @@ pub fn call_potential_snvs(
                                 'C' | 'c' => 1,
                                 'G' | 'g' => 2,
                                 'T' | 't' => 3,
-                                _ => 4
+                                _ => 4,
                             };
 
                             counts[b] += 1;
diff --git a/src/extract_fragments.rs b/src/extract_fragments.rs
index c40a4ec..5ea8206 100644
--- a/src/extract_fragments.rs
+++ b/src/extract_fragments.rs
@@ -32,10 +32,10 @@ use rust_htslib::bam::record::Cigar;
 use rust_htslib::bam::record::CigarStringView;
 use rust_htslib::bam::record::Record;
 use rust_htslib::bam::Read;
-use util::*;
-use variants_and_fragments::*;
 use std::u32;
 use std::usize;
+use util::*;
+use variants_and_fragments::*;
 
 static VERBOSE: bool = false;
 static IGNORE_INDEL_ONLY_CLUSTERS: bool = false;
@@ -66,7 +66,7 @@ pub struct ExtractFragmentParameters {
     pub max_cigar_indel: usize,
     /// whether or not to store the read id.
     /// we store the read ID if we'll be separating reads by haplotype and otherwise we don't
-    pub store_read_id: bool
+    pub store_read_id: bool,
 }
 
 /// an extension of the rust-htslib cigar representation that has the cigar operation and length as
@@ -794,7 +794,7 @@ fn extract_var_cluster(
             var_ix: var_cluster[v as usize].ix,
             allele: best_allele,
             qual: qual,
-            one_minus_qual: LogProb::ln_one_minus_exp(&qual)
+            one_minus_qual: LogProb::ln_one_minus_exp(&qual),
         });
     }
 
@@ -830,9 +830,8 @@ pub fn extract_fragment(
         id: Some(id),
         calls: vec![],
         // ln(0.5) stored as f16 for compactness
-        p_read_hap: [LogProb::from(Prob(0.5)),
-                     LogProb::from(Prob(0.5))],
-        reverse_strand: bam_record.is_reverse()
+        p_read_hap: [LogProb::from(Prob(0.5)), LogProb::from(Prob(0.5))],
+        reverse_strand: bam_record.is_reverse(),
     };
 
     if bam_record.is_quality_check_failed()
diff --git a/src/genotype_probs.rs b/src/genotype_probs.rs
index d900a72..dc95f9c 100644
--- a/src/genotype_probs.rs
+++ b/src/genotype_probs.rs
@@ -47,7 +47,6 @@ impl GenotypeProbs {
 
         for i in 0..self.n_alleles() {
             for j in 0..self.n_alleles() {
-
                 let post: LogProb = self.tab[i][j];
 
                 if post > max_post {
diff --git a/src/haplotype_assembly.rs b/src/haplotype_assembly.rs
index 0681293..864092f 100644
--- a/src/haplotype_assembly.rs
+++ b/src/haplotype_assembly.rs
@@ -21,7 +21,6 @@ pub fn separate_fragments_by_haplotype(
     let mut unassigned_count = 0;
 
     for ref f in flist {
-
         // we store p_read_hap as ln-scaled f16s to save space. need to convert back.
         let p_read_hap0 = LogProb(f64::from(f.p_read_hap[0]));
         let p_read_hap1 = LogProb(f64::from(f.p_read_hap[1]));
@@ -42,7 +41,9 @@ pub fn separate_fragments_by_haplotype(
                     unassigned_count += 1;
                 }
             }
-            &None => {bail!("Fragment without read ID found while separating reads by haplotype.");}
+            &None => {
+                bail!("Fragment without read ID found while separating reads by haplotype.");
+            }
         }
     }
 
@@ -176,8 +177,8 @@ pub fn generate_flist_buffer(
         line.push(' ' as u8);
 
         let fid = match &frag.id {
-            Some(ref fid) => {fid.clone()}
-            None => {frag_num.to_string()}
+            Some(ref fid) => fid.clone(),
+            None => frag_num.to_string(),
         };
 
         for u in fid.clone().into_bytes() {
@@ -251,7 +252,6 @@ extern "C" {
     );
 }
 
-
 pub fn call_hapcut2(
     frag_buffer: &Vec<Vec<u8>>,
     fragments: usize,
@@ -334,7 +334,8 @@ pub fn calculate_mec(
         match var.phase_set {
             Some(ps) => {
                 *block_mec.entry(ps).or_insert(0) += var.mec;
-                *block_total.entry(ps).or_insert(0) += var.allele_counts.iter().sum::<u16>() as usize;
+                *block_total.entry(ps).or_insert(0) +=
+                    var.allele_counts.iter().sum::<u16>() as usize;
             }
             None => {}
         }
@@ -344,13 +345,13 @@ pub fn calculate_mec(
         match var.phase_set {
             Some(ps) => {
                 var.mec_frac_block = *block_mec
+                    .get(&ps)
+                    .chain_err(|| "Error retrieving MEC for phase set.")?
+                    as f64
+                    / *block_total
                         .get(&ps)
                         .chain_err(|| "Error retrieving MEC for phase set.")?
-                        as f64
-                        / *block_total
-                            .get(&ps)
-                            .chain_err(|| "Error retrieving MEC for phase set.")?
-                            as f64;
+                        as f64;
                 var.mec_frac_variant =
                     var.mec as f64 / var.allele_counts.iter().sum::<u16>() as f64;
             }
diff --git a/src/main.rs b/src/main.rs
index 60c2ef9..a69dcf8 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -374,7 +374,8 @@ fn run() -> Result<()> {
     let min_allele_qual: f64 = parse_nonnegative_f64(&input_args, "Min allele quality")?;
     let strand_bias_pvalue_cutoff: f64 =
         parse_nonnegative_f64(&input_args, "Strand Bias P-value cutoff")?;
-    let hap_assignment_qual: f64 = parse_nonnegative_f64(&input_args, "Haplotype assignment quality")?;
+    let hap_assignment_qual: f64 =
+        parse_nonnegative_f64(&input_args, "Haplotype assignment quality")?;
     let ll_delta: f64 = parse_positive_f64(&input_args, "Haplotype Convergence Delta")?;
     let potential_snv_cutoff_phred = parse_positive_f64(&input_args, "Potential SNV Cutoff")?;
     let potential_snv_min_alt_count: usize =
@@ -528,7 +529,7 @@ fn run() -> Result<()> {
         variant_cluster_max_size: variant_cluster_max_size,
         max_window_padding,
         max_cigar_indel,
-        store_read_id
+        store_read_id,
     };
 
     eprintln!("{} Estimating alignment parameters...", print_time());
@@ -819,14 +820,15 @@ fn run() -> Result<()> {
     // write BAM files for h1,h2, and unassigned
     match hap_bam_prefix {
         Some(p) => {
-
             eprintln!(
                 "{} Calculating fraction of reads assigned to either haplotype...",
                 print_time()
             );
             // h1 and h2 are hash-sets containing the qnames of the reads assigned to haplotype 1 and 2 respectively.
-            let (h1, h2) =
-                separate_fragments_by_haplotype(&flist, LogProb::from(Prob(1.0 - hap_max_p_misassign)))?;
+            let (h1, h2) = separate_fragments_by_haplotype(
+                &flist,
+                LogProb::from(Prob(1.0 - hap_max_p_misassign)),
+            )?;
 
             eprintln!(
                 "{} Writing haplotype-assigned reads to bam files...",
diff --git a/src/realignment.rs b/src/realignment.rs
index f212784..da354f1 100644
--- a/src/realignment.rs
+++ b/src/realignment.rs
@@ -126,7 +126,6 @@ pub fn forward_algorithm_non_numerically_stable(
         middle_prev[j] = 0.0;
     }
 
-
     let t = params.transition_probs;
     let e = params.emission_probs;
 
@@ -143,19 +142,16 @@ pub fn forward_algorithm_non_numerically_stable(
             w.len()
         };
 
-
         if band_start == 1 {
             upper_curr[0] = 0.0;
             middle_curr[0] = 0.0;
             if i == 1 {
                 lower_curr[0] = params.transition_probs.insertion_from_match
             } else {
-                lower_curr[0] =
-                    lower_prev[0] * params.transition_probs.insertion_from_insertion;
+                lower_curr[0] = lower_prev[0] * params.transition_probs.insertion_from_insertion;
             }
         }
 
-
         for j in band_start..(band_end + 1) {
             let lower_continue = lower_prev[j] * t.insertion_from_insertion;
             let lower_from_middle = middle_prev[j] * t.insertion_from_match;
@@ -177,7 +173,7 @@ pub fn forward_algorithm_non_numerically_stable(
                 match_emission * (middle_from_lower + middle_continue + middle_from_upper);
         }
 
-        for j in (band_start-1)..(band_end + 1) {
+        for j in (band_start - 1)..(band_end + 1) {
             upper_prev[j] = upper_curr[j];
             middle_prev[j] = middle_curr[j];
             lower_prev[j] = lower_curr[j];
@@ -185,9 +181,9 @@ pub fn forward_algorithm_non_numerically_stable(
         // we previously had a bug at the left boundary of the band... set these to NaN to make sure they
         // aren't used again
         if band_start >= 2 {
-            upper_prev[band_start-2] = f64::NAN;
-            middle_prev[band_start-2] = f64::NAN;
-            lower_prev[band_start-2] = f64::NAN;
+            upper_prev[band_start - 2] = f64::NAN;
+            middle_prev[band_start - 2] = f64::NAN;
+            lower_prev[band_start - 2] = f64::NAN;
         }
 
         upper_curr[band_start] = 0.0;
@@ -245,8 +241,7 @@ pub fn forward_algorithm_numerically_stable(
             if i == 1 {
                 lower_curr[0] = params.transition_probs.insertion_from_match
             } else {
-                lower_curr[0] =
-                    lower_prev[0] + params.transition_probs.insertion_from_insertion;
+                lower_curr[0] = lower_prev[0] + params.transition_probs.insertion_from_insertion;
             }
         }
 
@@ -271,7 +266,7 @@ pub fn forward_algorithm_numerically_stable(
             middle_curr[j] = match_emission + LogProb::ln_sum_exp(&options3);
         }
 
-        for j in (band_start-1)..(band_end + 1) {
+        for j in (band_start - 1)..(band_end + 1) {
             upper_prev[j] = upper_curr[j];
             middle_prev[j] = middle_curr[j];
             lower_prev[j] = lower_curr[j];
@@ -279,9 +274,9 @@ pub fn forward_algorithm_numerically_stable(
         // we previously had a bug at the left boundary of the band... set these to NaN to make sure they
         // aren't used again
         if band_start >= 2 {
-            upper_prev[band_start-2] = LogProb(f64::NAN);
-            middle_prev[band_start-2] = LogProb(f64::NAN);
-            lower_prev[band_start-2] = LogProb(f64::NAN);
+            upper_prev[band_start - 2] = LogProb(f64::NAN);
+            middle_prev[band_start - 2] = LogProb(f64::NAN);
+            lower_prev[band_start - 2] = LogProb(f64::NAN);
         }
 
         upper_curr[band_start] = LogProb::ln_zero();
@@ -317,7 +312,6 @@ pub fn viterbi_max_scoring_alignment(
         upper_prev[j] = upper_prev[j - 1] + params.transition_probs.deletion_from_deletion;
     }
 
-
     for i in 1..(v.len() + 1) {
         let band_middle = (w.len() * i) / v.len();
         let band_start = if band_middle >= band_width / 2 + 1 {
@@ -336,12 +330,10 @@ pub fn viterbi_max_scoring_alignment(
             if i == 1 {
                 lower_curr[0] = params.transition_probs.insertion_from_match
             } else {
-                lower_curr[0] =
-                    lower_prev[0] + params.transition_probs.insertion_from_insertion;
+                lower_curr[0] = lower_prev[0] + params.transition_probs.insertion_from_insertion;
             }
         }
 
-
         for j in band_start..(band_end + 1) {
             let lower_continue = lower_prev[j] + t.insertion_from_insertion;
             let lower_from_middle = middle_prev[j] + t.insertion_from_match;
@@ -377,7 +369,7 @@ pub fn viterbi_max_scoring_alignment(
             middle_curr[j] = match_emission + max_option;
         }
 
-        for j in (band_start-1)..(band_end + 1) {
+        for j in (band_start - 1)..(band_end + 1) {
             upper_prev[j] = upper_curr[j];
             middle_prev[j] = middle_curr[j];
             lower_prev[j] = lower_curr[j];
@@ -385,9 +377,9 @@ pub fn viterbi_max_scoring_alignment(
         // we previously had a bug at the left boundary of the band... set these to NaN to make sure they
         // aren't used again
         if band_start >= 2 {
-            upper_prev[band_start-2] = LogProb(f64::NAN);
-            middle_prev[band_start-2] = LogProb(f64::NAN);
-            lower_prev[band_start-2] = LogProb(f64::NAN);
+            upper_prev[band_start - 2] = LogProb(f64::NAN);
+            middle_prev[band_start - 2] = LogProb(f64::NAN);
+            lower_prev[band_start - 2] = LogProb(f64::NAN);
         }
 
         upper_curr[band_start] = LogProb::ln_zero();
diff --git a/src/variants_and_fragments.rs b/src/variants_and_fragments.rs
index fe3704d..7171d2e 100644
--- a/src/variants_and_fragments.rs
+++ b/src/variants_and_fragments.rs
@@ -16,11 +16,11 @@ use util::*;
 
 #[derive(Clone, Copy)]
 pub struct FragCall {
-    pub frag_ix: usize,  // index into fragment list
+    pub frag_ix: usize,          // index into fragment list
     pub var_ix: usize,           // index into variant list
     pub allele: u8,              // allele call
     pub qual: LogProb,           // LogProb probability the call is an error
-    pub one_minus_qual: LogProb,           // LogProb 1-probability the call is an error
+    pub one_minus_qual: LogProb, // LogProb 1-probability the call is an error
 }
 
 #[derive(Clone)]
@@ -28,7 +28,7 @@ pub struct Fragment {
     pub id: Option<String>,
     pub calls: Vec<FragCall>,
     pub p_read_hap: [LogProb; 2],
-    pub reverse_strand: bool
+    pub reverse_strand: bool,
 }
 
 #[repr(u8)]
@@ -110,7 +110,7 @@ pub struct Var {
     // e.g. genotype_posteriors[2][0] is the log posterior probability of 2|0 haplotype
     pub phase_set: Option<usize>,
     pub strand_bias_pvalue: f64, // fisher's exact test strand bias Pvalue
-    pub mec: usize,                // mec for variant
+    pub mec: usize,              // mec for variant
     pub mec_frac_variant: f64,   // mec fraction for this variant
     pub mec_frac_block: f64,     // mec fraction for this haplotype block
     pub mean_allele_qual: f64,
@@ -244,7 +244,7 @@ pub fn parse_vcf_potential_variants(
             mq20_frac: 0.0,
             mq30_frac: 0.0,
             mq40_frac: 0.0,
-            mq50_frac: 0.0
+            mq50_frac: 0.0,
         };
         varlist.push(new_var);
     }